Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001030375.1| pentatricopeptide repeat-containing protein ... 599 e-171
Alignment gi|NP_001033197.1| 28S ribosomal protein S27, mitochondrial [Bo... 54 4e-07
>ref|NP_001030375.1| pentatricopeptide repeat-containing protein 2 [Bos taurus].
Length = 384
Score = 599 bits (1545), Expect = e-171
Identities = 301/363 (82%), Positives = 328/363 (90%)
Frame = +2
Query: 83 WPGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVACNLPGTKETYLRNLEEKLT 262
W G SGSTCC CPLGAKRYLLT++I+KLKEFQ KKVAVACNLPGTKETYLRNLEEKLT
Sbjct: 24 WVG--GSGSTCCLCPLGAKRYLLTDSIVKLKEFQRKKVAVACNLPGTKETYLRNLEEKLT 81
Query: 263 QNKLILKEELRTLLHLCESRDDMELAKNVIYRYHAENRNMTVGEYKFGPLFMRLCYELDL 442
QNKLILKEELRTLLHLC SRDD+ELAK+VIYRYHAENRN+T+GEYKFGPLF+RLCYELDL
Sbjct: 82 QNKLILKEELRTLLHLCTSRDDVELAKHVIYRYHAENRNITLGEYKFGPLFVRLCYELDL 141
Query: 443 EESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFSKDTYVL 622
E+SAVELIKDQHL+GFFSD TSFNILMD LFIKGKY+SALEV+I+MKNQD+KF+KDTYVL
Sbjct: 142 EDSAVELIKDQHLQGFFSDSTSFNILMDMLFIKGKYRSALEVLIQMKNQDLKFNKDTYVL 201
Query: 623 AFAVCYKLNSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAKALSIFSQIM 802
AFA+CYKLNSPESF+ICTTLREEALIKGE+L RRASCFAVALALNQNQ AKA+SIFSQIM
Sbjct: 202 AFAICYKLNSPESFQICTTLREEALIKGEILPRRASCFAVALALNQNQVAKAISIFSQIM 261
Query: 803 KPESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFSXXXXXXXXXXXXXX 982
PESIICTNLNIMIH+QSNMLK LI+ILKDATEGNLSRFVK+HVFS
Sbjct: 262 NPESIICTNLNIMIHIQSNMLKTLIDILKDATEGNLSRFVKRHVFSEEVLVKVREKVKDV 321
Query: 983 PALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRRTFQPLSQSL 1162
PALLA+FDEL KLH +GQVT Y+LDALLCHTP D +S+ LLNKRTVSRRTFQPLSQSL
Sbjct: 322 PALLAEFDELNKKLHRSGQVTAYTLDALLCHTPSDRQSYTVLLNKRTVSRRTFQPLSQSL 381
Query: 1163 WAE 1171
WAE
Sbjct: 382 WAE 384
>ref|NP_001033197.1| 28S ribosomal protein S27, mitochondrial [Bos taurus].
Length = 415
Score = 53.9 bits (128), Expect = 4e-07
Identities = 44/177 (24%), Positives = 83/177 (46%), Gaps = 5/177 (2%)
Frame = +2
Query: 128 LGAKRYLLTENIMKLKEFQHKKVAVACNLPGTKETYLRNLEEKLTQNKLILKEELRTLLH 307
L KRYLL+ ++++ + C+L + E KL + L + + +
Sbjct: 23 LAGKRYLLSAAYEDSRKWE-ARAKEDCHLADLASLMDKTYERKLPVSSLTISRFVDNI-- 79
Query: 308 LCESRDDMELAKNVIYRY-HAEN----RNMTVGEYKFGPLFMRLCYELDLEESAVELIKD 472
SR++++ A+ +Y++ H+ N RN T+ + +R C + ++ A+ + +
Sbjct: 80 --SSREEIDHAEYYLYKFRHSPNCWYLRNWTIHTW------IRQCLKYGAQDKALYTLVN 131
Query: 473 QHLRGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFSKDTYVLAFAVCYK 643
+ G F D +FN+LMD K YK AL V+ E+ Q+ T +L+ V Y+
Sbjct: 132 KVQYGIFPDNYTFNLLMDHFIKKENYKDALSVVFEIMMQEAFEVPSTQLLSLYVLYQ 188
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 60,046,648
Number of extensions: 1699508
Number of successful extensions: 5218
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 5214
Number of HSP's successfully gapped: 2
Length of query: 516
Length of database: 17,681,374
Length adjustment: 107
Effective length of query: 409
Effective length of database: 14,140,958
Effective search space: 5783651822
Effective search space used: 5783651822
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_852983.1| PREDICTED: similar to pentatricopeptide repeat ... 579 e-165
>ref|XP_852983.1| PREDICTED: similar to pentatricopeptide repeat domain 2 [Canis
familiaris].
Length = 383
Score = 579 bits (1493), Expect = e-165
Identities = 287/362 (79%), Positives = 318/362 (87%)
Frame = +2
Query: 86 PGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVACNLPGTKETYLRNLEEKLTQ 265
PG + SGS CRCPLGAKRYLLT+N +KLKEFQHKKVA+A +LPGTK TYLRN+EEKLT
Sbjct: 22 PGAVGSGSAGCRCPLGAKRYLLTDNTVKLKEFQHKKVAIASHLPGTKATYLRNVEEKLTH 81
Query: 266 NKLILKEELRTLLHLCESRDDMELAKNVIYRYHAENRNMTVGEYKFGPLFMRLCYELDLE 445
NKLIL+EELR LLHLC+SRDDMELAK IYRYHAENRN+T G+YKFGPLFMRLCYELDLE
Sbjct: 82 NKLILREELRILLHLCDSRDDMELAKKAIYRYHAENRNVTFGDYKFGPLFMRLCYELDLE 141
Query: 446 ESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFSKDTYVLA 625
ESA+ELIKDQHLRGFFSD TSFNILMD LFIKG+Y SALEV+IEMKNQDVKF+KDTYVLA
Sbjct: 142 ESALELIKDQHLRGFFSDSTSFNILMDMLFIKGRYSSALEVLIEMKNQDVKFNKDTYVLA 201
Query: 626 FAVCYKLNSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAKALSIFSQIMK 805
FA+CYKLNSPES KICTTLREEALIKGEVLSRRASCFAVALALNQNQ AKA SIFSQIMK
Sbjct: 202 FAICYKLNSPESLKICTTLREEALIKGEVLSRRASCFAVALALNQNQVAKATSIFSQIMK 261
Query: 806 PESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFSXXXXXXXXXXXXXXP 985
PES++C NL I+IH+++NMLKALI+ILKDATEGNLS+FVK+ FS P
Sbjct: 262 PESVLCANLKILIHIKANMLKALIQILKDATEGNLSKFVKRPEFSEEVLAKAREKVKDVP 321
Query: 986 ALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRRTFQPLSQSLW 1165
ALLA+FDE+Y KL ++GQ+TTY+LD LLCHTP D KSHM LLNKRTVS RT QPL+QSLW
Sbjct: 322 ALLARFDEIYEKLQISGQITTYTLDTLLCHTPGDRKSHMILLNKRTVSHRTCQPLNQSLW 381
Query: 1166 AE 1171
AE
Sbjct: 382 AE 383
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 62,491,922
Number of extensions: 1748617
Number of successful extensions: 5744
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 5736
Number of HSP's successfully gapped: 1
Length of query: 516
Length of database: 18,874,504
Length adjustment: 107
Effective length of query: 409
Effective length of database: 15,307,552
Effective search space: 6260788768
Effective search space used: 6260788768
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_079030.3| pentatricopeptide repeat-containing protein 2 [... 583 e-166
Alignment gi|NP_055899.2| 28S ribosomal protein S27, mitochondrial [Homo ... 55 2e-07
>ref|NP_079030.3| pentatricopeptide repeat-containing protein 2 [Homo sapiens].
Length = 388
Score = 583 bits (1502), Expect = e-166
Identities = 297/385 (77%), Positives = 328/385 (85%), Gaps = 2/385 (0%)
Frame = +2
Query: 23 DNMAAAFXXXXXXXXXXXXX--WPGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKV 196
D+MAAAF +PGV SGS CRCPLGAKRYLLT+N++KLKEFQ KKV
Sbjct: 4 DSMAAAFRPSNRVLLQALQILVYPGVGGSGSVSCRCPLGAKRYLLTDNVVKLKEFQQKKV 63
Query: 197 AVACNLPGTKETYLRNLEEKLTQNKLILKEELRTLLHLCESRDDMELAKNVIYRYHAENR 376
AVACNL GTKETY RNL++KLTQNKLILK EL TLLHLCESRD +ELAKNVIYRYHAEN+
Sbjct: 64 AVACNLSGTKETYFRNLKKKLTQNKLILKGELITLLHLCESRDHVELAKNVIYRYHAENK 123
Query: 377 NMTVGEYKFGPLFMRLCYELDLEESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKYKS 556
N T+GEYKFGPLF+RLCYELDLEESAVEL+KDQHLRGFFSD TSFNILMD LFIKGKYKS
Sbjct: 124 NFTLGEYKFGPLFVRLCYELDLEESAVELMKDQHLRGFFSDSTSFNILMDMLFIKGKYKS 183
Query: 557 ALEVMIEMKNQDVKFSKDTYVLAFAVCYKLNSPESFKICTTLREEALIKGEVLSRRASCF 736
AL+V+IEMKNQDVKF+KDTYVLAFA+CYKLNSPESFKICTTLREEAL+KGE+LSRRASCF
Sbjct: 184 ALQVLIEMKNQDVKFTKDTYVLAFAICYKLNSPESFKICTTLREEALLKGEILSRRASCF 243
Query: 737 AVALALNQNQPAKALSIFSQIMKPESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSR 916
AVALALNQN+ AKA+SIFSQIM PESI C NLNI+IH+QSNML+ LI+ LK+A EGNLS+
Sbjct: 244 AVALALNQNEMAKAVSIFSQIMNPESIACINLNIIIHIQSNMLENLIKTLKNAAEGNLSK 303
Query: 917 FVKKHVFSXXXXXXXXXXXXXXPALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKS 1096
FVK+HVFS PAL+AKFDE+YG LH+ GQVTT SLDA+LCHTPRD KS
Sbjct: 304 FVKRHVFSEEVLAKVREKVKDVPALVAKFDEIYGTLHITGQVTTDSLDAVLCHTPRDRKS 363
Query: 1097 HMGLLNKRTVSRRTFQPLSQSLWAE 1171
H LLNKR VSRRTFQPLSQSL AE
Sbjct: 364 HTLLLNKRMVSRRTFQPLSQSLLAE 388
>ref|NP_055899.2| 28S ribosomal protein S27, mitochondrial [Homo sapiens].
Length = 414
Score = 54.7 bits (130), Expect = 2e-07
Identities = 44/173 (25%), Positives = 83/173 (47%), Gaps = 5/173 (2%)
Frame = +2
Query: 137 KRYLLTENIMKLKEFQHKKVAVACNLPGTKETYLRNLEEKLTQNKLILKEELRTLLHLCE 316
KRYLL+ + +++ ++ C L + E KL + L + L+
Sbjct: 26 KRYLLSSAYVDSHKWEAREKEHYC-LADLASLMDKTFERKLPVSSLTISR----LIDNIS 80
Query: 317 SRDDMELAKNVIYRY-HAEN----RNMTVGEYKFGPLFMRLCYELDLEESAVELIKDQHL 481
SR++++ A+ +Y++ H+ N RN T+ + +R C + D ++ A+ + ++
Sbjct: 81 SREEIDHAEYYLYKFRHSPNCWYLRNWTIHTW------IRQCLKYDAQDKALYTLVNKVQ 134
Query: 482 RGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFSKDTYVLAFAVCY 640
G F D +FN+LMD+ K YK AL V+ E+ Q+ T +L+ V +
Sbjct: 135 YGIFPDNFTFNLLMDSFIKKENYKDALSVVFEVMMQEAFEVPSTQLLSLYVLF 187
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 61,478,407
Number of extensions: 1722288
Number of successful extensions: 5379
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 5373
Number of HSP's successfully gapped: 2
Length of query: 516
Length of database: 18,297,164
Length adjustment: 107
Effective length of query: 409
Effective length of database: 14,770,016
Effective search space: 6040936544
Effective search space used: 6040936544
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_081149.1| pentatricopeptide repeat-containing protein 2 [... 533 e-151
Alignment gi|NP_776118.2| 28S ribosomal protein S27, mitochondrial [Mus m... 53 6e-07
>ref|NP_081149.1| pentatricopeptide repeat-containing protein 2 [Mus musculus].
Length = 381
Score = 533 bits (1373), Expect = e-151
Identities = 256/362 (70%), Positives = 310/362 (85%)
Frame = +2
Query: 86 PGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVACNLPGTKETYLRNLEEKLTQ 265
PGV SGS CCRC LGAKRYLLT+NI+KLKEFQHKK+A+A NLPGTKE Y RNLEEKLTQ
Sbjct: 20 PGVTGSGSACCRCTLGAKRYLLTDNIVKLKEFQHKKIAIAYNLPGTKEIYFRNLEEKLTQ 79
Query: 266 NKLILKEELRTLLHLCESRDDMELAKNVIYRYHAENRNMTVGEYKFGPLFMRLCYELDLE 445
NKLILKEEL+TLL+LC+S +D++LAK VIYRYHAEN+N T+GEYKFGP+FMRLCYELDLE
Sbjct: 80 NKLILKEELKTLLYLCQSLEDVQLAKAVIYRYHAENKNFTLGEYKFGPVFMRLCYELDLE 139
Query: 446 ESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFSKDTYVLA 625
+SAVEL++D+HL+GFF D TSFNILMD LF KGKY+ AL+V+IEMKNQDV+FSK+TY+LA
Sbjct: 140 DSAVELVRDKHLQGFFLDSTSFNILMDMLFTKGKYERALQVLIEMKNQDVRFSKETYILA 199
Query: 626 FAVCYKLNSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAKALSIFSQIMK 805
FA+CYKLN+ ES KICTTLREEALIKG+++ RRA CF VALALN+NQ A+SIFSQI+
Sbjct: 200 FAICYKLNTLESLKICTTLREEALIKGDIICRRAYCFVVALALNKNQLKNAVSIFSQIVN 259
Query: 806 PESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFSXXXXXXXXXXXXXXP 985
PESI+C NLNI+IH+QSNML++L++IL+D+ + NLS+FV++H FS P
Sbjct: 260 PESIVCINLNILIHIQSNMLESLLKILEDSLDTNLSKFVRRHTFSEEVLAKVREKLKDSP 319
Query: 986 ALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRRTFQPLSQSLW 1165
AL+A+FDE+YGKLHVNGQ+T +SLDALLCH PRD +S++ LL KR VS RT QPLS+SL
Sbjct: 320 ALIARFDEVYGKLHVNGQITVHSLDALLCHVPRDKRSNLLLLKKRAVSHRTLQPLSRSLL 379
Query: 1166 AE 1171
E
Sbjct: 380 TE 381
>ref|NP_776118.2| 28S ribosomal protein S27, mitochondrial [Mus musculus].
Length = 415
Score = 53.1 bits (126), Expect = 6e-07
Identities = 49/193 (25%), Positives = 89/193 (46%), Gaps = 10/193 (5%)
Frame = +2
Query: 95 LDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVACNLPGTKETY----LRNLEEKLT 262
LD+ C L KR LL+ + +++ ++ KE Y L +L +K
Sbjct: 16 LDASRLC----LAGKRCLLSAAYVDSHQWEARE----------KEEYHLADLASLMDKAY 61
Query: 263 QNKLILKE-ELRTLLHLCESRDDMELAKNVIYRY-HAEN----RNMTVGEYKFGPLFMRL 424
+ KL + + + SR+D++ A+ +Y++ H+ N R+ T+ + +R
Sbjct: 62 ERKLPVSSLSISRFVDNIASREDLDSAEYYLYKFRHSPNCWYLRDWTIHSW------IRQ 115
Query: 425 CYELDLEESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKYKSALEVMIEMKNQDVKFS 604
C + ++ A+ + ++ G F D +FN+LMD KG YK AL V+ E+ Q+
Sbjct: 116 CLKYGAQDKALYTLVNKVQYGIFPDNFTFNLLMDYFIKKGNYKDALSVVFEIMMQEAFDV 175
Query: 605 KDTYVLAFAVCYK 643
T L+ V Y+
Sbjct: 176 PSTQFLSLYVLYR 188
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 52,309,529
Number of extensions: 1449818
Number of successful extensions: 4587
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 4584
Number of HSP's successfully gapped: 2
Length of query: 516
Length of database: 15,617,559
Length adjustment: 106
Effective length of query: 410
Effective length of database: 12,433,743
Effective search space: 5097834630
Effective search space used: 5097834630
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 36 (18.5 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003134082.2| PREDICTED: pentatricopeptide repeat-containi... 313 2e-85
Alignment gi|XP_003134081.1| PREDICTED: 28S ribosomal protein S27, mitoch... 51 2e-06
>ref|XP_003134082.2| PREDICTED: pentatricopeptide repeat-containing protein 2-like [Sus
scrofa].
Length = 276
Score = 313 bits (801), Expect = 2e-85
Identities = 166/192 (86%), Positives = 167/192 (86%)
Frame = +2
Query: 596 KFSKDTYVLAFAVCYKLNSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAK 775
K SKD L+ NSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAK
Sbjct: 92 KASKDKQPLS-------NSPESFKICTTLREEALIKGEVLSRRASCFAVALALNQNQPAK 144
Query: 776 ALSIFSQIMKPESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFSXXXXX 955
ALSIFSQIMKPESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFS
Sbjct: 145 ALSIFSQIMKPESIICTNLNIMIHVQSNMLKALIEILKDATEGNLSRFVKKHVFSEEVLV 204
Query: 956 XXXXXXXXXPALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRR 1135
PALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRR
Sbjct: 205 KVREKVKHVPALLAKFDELYGKLHVNGQVTTYSLDALLCHTPRDVKSHMGLLNKRTVSRR 264
Query: 1136 TFQPLSQSLWAE 1171
TFQPLSQSLWAE
Sbjct: 265 TFQPLSQSLWAE 276
Score = 110 bits (276), Expect = 2e-24
Identities = 53/66 (80%), Positives = 53/66 (80%)
Frame = +2
Query: 29 MAAAFXXXXXXXXXXXXXWPGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVAC 208
MAAAF WPGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVAC
Sbjct: 1 MAAAFRSSQQVLLLRSLVWPGVLDSGSTCCRCPLGAKRYLLTENIMKLKEFQHKKVAVAC 60
Query: 209 NLPGTK 226
NLPGTK
Sbjct: 61 NLPGTK 66
>ref|XP_003134081.1| PREDICTED: 28S ribosomal protein S27, mitochondrial-like [Sus
scrofa].
Length = 415
Score = 51.2 bits (121), Expect = 2e-06
Identities = 39/150 (26%), Positives = 71/150 (47%), Gaps = 5/150 (3%)
Frame = +2
Query: 206 CNLPGTKETYLRNLEEKLTQNKLILKEELRTLLHLCESRDDMELAKNVIYRY-HAEN--- 373
C+L + E KL + L + + + SR+D++ A+ +Y++ H+ N
Sbjct: 48 CHLADLASLMDKTYERKLPVSSLTISRFVDNIA----SREDIDHAEYYLYKFRHSPNCWY 103
Query: 374 -RNMTVGEYKFGPLFMRLCYELDLEESAVELIKDQHLRGFFSDCTSFNILMDTLFIKGKY 550
R+ T+ + +R C + ++ A+ +K++ G F D +FN+LMD K Y
Sbjct: 104 LRDWTIHTW------IRQCLKYGAQDKALYTLKNKVQYGIFPDNYTFNLLMDYFIKKENY 157
Query: 551 KSALEVMIEMKNQDVKFSKDTYVLAFAVCY 640
K AL V+ E+ Q+ T +L+ V Y
Sbjct: 158 KDALSVVFEIMMQEAFEVPSTQLLSLYVLY 187
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 38,647,381
Number of extensions: 1092003
Number of successful extensions: 3536
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 3535
Number of HSP's successfully gapped: 3
Length of query: 516
Length of database: 11,343,932
Length adjustment: 103
Effective length of query: 413
Effective length of database: 8,779,541
Effective search space: 3625950433
Effective search space used: 3625950433
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-003406
(1549 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr16 1112 0.0
>Sscrofa_Chr16
|| Length = 86898991
Score = 1112 bits (561), Expect = 0.0
Identities = 582/589 (98%)
Strand = Plus / Minus
Query: 949 gctggtcaaagtgagggaaaaggtgaagcacgtgcctgctcttctggccaaatttgacga 1008
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738623 gctggtcaaagtgagggaaaaggtgaagcacgtgcctgctcttctggccaaatttgacga 52738564
Query: 1009 gctctatgggaaactgcacgtaaatggccaggtcacaacttacagtttggatgctctgct 1068
|||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 52738563 gctctatgggaaactgcacgtaaatggccaggtcacgacttacagtttggatgctctgct 52738504
Query: 1069 ctgccacacgcccagggacgtgaaatcccacatggggctgctcaacaagaggacagtcag 1128
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738503 ctgccacacgcccagggacgtgaaatcccacatggggctgctcaacaagaggacagtcag 52738444
Query: 1129 ccgtcggaccttccagccactcagccagtccctgtgggccgaataaccctgggttcaaac 1188
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738443 ccgtcggaccttccagccactcagccagtccctgtgggccgaataaccctgggttcaaac 52738384
Query: 1189 cagccgtgggcctgagttggaggggcctgcctctagtgagttactggcttcctaagaagt 1248
||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 52738383 cagccgtgggcctgagttggaggggcctgcctctagtgaattactggcttcctaagaagt 52738324
Query: 1249 caggcatcccactccggtgcatcctctcctaacccctggtctcctccttcaatctccacg 1308
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738323 caggcatcccactccggtgcatcctctcctaacccctggtctcctccttcaatctccaca 52738264
Query: 1309 ttcactgactgctggcaggctgacttgagaagttcaaggtgtgccgttgtgaagcaagca 1368
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738263 ttcactgactgctggcaggctgacttgagaagttcaaggtgtgccgttgtgaagcaagca 52738204
Query: 1369 cagcagaaagcttgaccccccgcggaaaggaggcttccctgcacagactgccgcggatcc 1428
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738203 cagcagaaagcttggccccccgcggaaaggaggcttccctgcacagactgccgcggatcc 52738144
Query: 1429 tcggaaggacacggtcacggtcaccgtgttcagcccagcttctgtaccagagcagaaccc 1488
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52738143 tcggagggacacggtcacggtcaccgtgttcagcccagcttctgtaccagagcagaaccc 52738084
Query: 1489 aggaagcactcgctggcagggaggaatttcaccggaattcgccagctcc 1537
|||||||||||||||||||| |||||||||||||||| |||||||||||
Sbjct: 52738083 aggaagcactcgctggcaggaaggaatttcaccggaagtcgccagctcc 52738035
Score = 266 bits (134), Expect = 3e-68
Identities = 134/134 (100%)
Strand = Plus / Plus
Query: 1 tccctcagttggcgcagcccttgacaacatggctgccgcctttcggtcctcgcagcaagt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52593681 tccctcagttggcgcagcccttgacaacatggctgccgcctttcggtcctcgcagcaagt 52593740
Query: 61 tctgctgctgcggagtttggtgtggcccggggtcttggactcaggctccacgtgctgccg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52593741 tctgctgctgcggagtttggtgtggcccggggtcttggactcaggctccacgtgctgccg 52593800
Query: 121 ctgccctctcggag 134
||||||||||||||
Sbjct: 52593801 ctgccctctcggag 52593814
Score = 266 bits (134), Expect = 3e-68
Identities = 134/134 (100%)
Strand = Plus / Plus
Query: 226 agaaacctatttgagaaacttggaagagaagttgacccagaacaagctcatcttgaaaga 285
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52600584 agaaacctatttgagaaacttggaagagaagttgacccagaacaagctcatcttgaaaga 52600643
Query: 286 ggaattgagaaccttgcttcacctgtgtgagtcccgggatgacatggagctggctaaaaa 345
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52600644 ggaattgagaaccttgcttcacctgtgtgagtcccgggatgacatggagctggctaaaaa 52600703
Query: 346 cgtcatttacaggt 359
||||||||||||||
Sbjct: 52600704 cgtcatttacaggt 52600717
Score = 240 bits (121), Expect = 2e-60
Identities = 121/121 (100%)
Strand = Plus / Plus
Query: 355 caggtaccatgcagagaataggaatatgactgtgggggagtataagtttggaccgctgtt 414
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52604833 caggtaccatgcagagaataggaatatgactgtgggggagtataagtttggaccgctgtt 52604892
Query: 415 catgaggctgtgctacgagctggatctggaggagtctgcagtggagctcatcaaagacca 474
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52604893 catgaggctgtgctacgagctggatctggaggagtctgcagtggagctcatcaaagacca 52604952
Query: 475 g 475
|
Sbjct: 52604953 g 52604953
Score = 228 bits (115), Expect = 7e-57
Identities = 115/115 (100%)
Strand = Plus / Plus
Query: 646 gaatagccctgaatcttttaaaatctgtaccacattaagagaagaagccctaatcaaagg 705
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52611228 gaatagccctgaatcttttaaaatctgtaccacattaagagaagaagccctaatcaaagg 52611287
Query: 706 agaagtcctctccaggagagcatcctgttttgcagtggcgctagctctgaaccag 760
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52611288 agaagtcctctccaggagagcatcctgttttgcagtggcgctagctctgaaccag 52611342
Score = 226 bits (114), Expect = 3e-56
Identities = 114/114 (100%)
Strand = Plus / Plus
Query: 836 attatgatccatgtccaatccaatatgctgaaagccctcatagaaatcctgaaggatgcc 895
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52620164 attatgatccatgtccaatccaatatgctgaaagccctcatagaaatcctgaaggatgcc 52620223
Query: 896 acagagggaaatttatcaagatttgtgaaaaaacatgtgttctcagaagaagtg 949
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52620224 acagagggaaatttatcaagatttgtgaaaaaacatgtgttctcagaagaagtg 52620277
Score = 188 bits (95), Expect = 6e-45
Identities = 95/95 (100%)
Strand = Plus / Plus
Query: 133 agctaaaagatacctacttacggagaatattatgaaattaaaagaattccagcataagaa 192
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52595053 agctaaaagatacctacttacggagaatattatgaaattaaaagaattccagcataagaa 52595112
Query: 193 ggtggctgttgcatgtaatcttcctggcaccaaag 227
|||||||||||||||||||||||||||||||||||
Sbjct: 52595113 ggtggctgttgcatgtaatcttcctggcaccaaag 52595147
Score = 182 bits (92), Expect = 4e-43
Identities = 92/92 (100%)
Strand = Plus / Plus
Query: 555 gtgcattggaagtaatgattgagatgaaaaaccaagatgtgaagttcagcaaagacacct 614
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52608353 gtgcattggaagtaatgattgagatgaaaaaccaagatgtgaagttcagcaaagacacct 52608412
Query: 615 acgttcttgcttttgcagtttgctacaaattg 646
||||||||||||||||||||||||||||||||
Sbjct: 52608413 acgttcttgcttttgcagtttgctacaaattg 52608444
Score = 165 bits (83), Expect = 9e-38
Identities = 83/83 (100%)
Strand = Plus / Plus
Query: 474 agcatttacgaggtttcttctcagactgcacatcattcaatattttgatggatacattgt 533
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52607854 agcatttacgaggtttcttctcagactgcacatcattcaatattttgatggatacattgt 52607913
Query: 534 ttatcaaaggcaaatataaaagt 556
|||||||||||||||||||||||
Sbjct: 52607914 ttatcaaaggcaaatataaaagt 52607936
Score = 153 bits (77), Expect = 3e-34
Identities = 77/77 (100%)
Strand = Plus / Plus
Query: 759 agaaccagccagcaaaggctctatccattttttctcaaatcatgaagccggaaagcataa 818
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52613237 agaaccagccagcaaaggctctatccattttttctcaaatcatgaagccggaaagcataa 52613296
Query: 819 tctgcactaatttaaat 835
|||||||||||||||||
Sbjct: 52613297 tctgcactaatttaaat 52613313
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 48,027,460
Number of extensions: 249
Number of successful extensions: 249
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 10
Length of query: 1549
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1528
Effective length of database: 2,808,413,156
Effective search space: 4291255302368
Effective search space used: 4291255302368
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)