BLASTP 2.2.26 [Sep-21-2011]
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy4856
(654 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 228 bits (582), Expect = 7e-60, Method: Compositional matrix adjust.
Identities = 134/387 (34%), Positives = 207/387 (53%), Gaps = 45/387 (11%)
Query: 6 SNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHLES-AVRVILL 64
S+ ++F VF NE T+VE+ P E++NDRNDRA+R+ WY EHL+ + V+L+
Sbjct: 115 SDDHKRFIVFHNEFSEHTFVERLPNETINDRNDRAIRKTCQWY---SEHLKPYDINVVLV 171
Query: 65 SEDVRNRDLAT---QSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSL----Y 117
+ D NR+ AT +S ++T S+ YI L N + + D + + ++ + +D+ +
Sbjct: 172 TNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTF 231
Query: 118 PLHATPSEIHAGIKNQSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDT 177
P + + + + G+KN L QG+ Q S NFLEG V+ + KP+L+ G++ LNRA +GD
Sbjct: 232 PEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQ 291
Query: 178 VAVRLLPESQWSAPXX----------------------XXXXXXXXXXXXXXXXXKLIKG 215
V V LLP+S+W AP +L+
Sbjct: 292 VIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAK 351
Query: 216 NKTVPPAERR--PTGQIVGIIKRKWRQYCGILQP---NPLAGSSRHLFVP-AERKIPKIR 269
+ + ++ PT ++V I +R WRQY G L P +P + S++++FV ++ +PK+R
Sbjct: 352 DAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVR 411
Query: 270 VETRQIATLSGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKF 329
+ TR+ A L +RIV++IDSWP +YP GHFVR LG I E E LLLEHDV + F
Sbjct: 412 IRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPF 471
Query: 330 SDLVLSYLPPMPWEKSTGRPWCSGTSI 356
S VL LP + G W + T +
Sbjct: 472 SKKVLECLP------AEGHDWKAPTKL 492
Score = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 35/72 (48%), Positives = 42/72 (58%)
Query: 402 LFQAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLL 461
+ A YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG + +
Sbjct: 789 MMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHR 848
Query: 462 DKKASTALCYNL 473
DK +C N+
Sbjct: 849 DKNKMDMICRNI 860
Score = 68.9 bits (167), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 42/134 (31%), Positives = 53/134 (39%), Gaps = 47/134 (35%)
Query: 476 DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLPGC 535
DF HYGLA IYTHFTSPIRRY D++ HR LA IG + + DK +C N
Sbjct: 804 DFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRN---- 859
Query: 536 TDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVA 595
+N ++R AQ+AGRAS+
Sbjct: 860 -------------------------------------------INRKHRNAQFAGRASIE 876
Query: 596 LHTHLFFRRKSITE 609
+ R TE
Sbjct: 877 YYVGQVMRNNESTE 890
Score = 59.7 bits (143), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 24/39 (61%), Positives = 30/39 (76%)
Query: 612 VARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
+ +R DLR +CS+DPPGC DI+DALH + LPNGN EV
Sbjct: 504 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEV 542
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/22 (72%), Positives = 18/22 (81%)
Query: 533 PGCTDIDDALHCRPLPNGNIEV 554
PGC DI+DALH + LPNGN EV
Sbjct: 521 PGCVDINDALHAKKLPNGNWEV 542
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 226 bits (577), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 133/387 (34%), Positives = 207/387 (53%), Gaps = 45/387 (11%)
Query: 6 SNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHLES-AVRVILL 64
S+ ++F VF NE T+VE+ P E++NDRN+RA+R+ WY EHL+ + V+L+
Sbjct: 141 SDDHKRFIVFHNEFSEHTFVERLPNETINDRNNRAIRKTCQWY---SEHLKPYDINVVLV 197
Query: 65 SEDVRNRDLAT---QSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSL----Y 117
+ D NR+ AT +S ++T S+ YI L N + + D + + ++ + +D+ +
Sbjct: 198 TNDRLNREAATKEVESNIITKSLVQYIELLPNADDIRDSIPQMDSFDKDLERDTFSDFTF 257
Query: 118 PLHATPSEIHAGIKNQSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDT 177
P + + + + G+KN L QG+ Q S NFLEG V+ + KP+L+ G++ LNRA +GD
Sbjct: 258 PEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQ 317
Query: 178 VAVRLLPESQWSAPXX----------------------XXXXXXXXXXXXXXXXXKLIKG 215
V V LLP+S+W AP +L+
Sbjct: 318 VIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRRLLAK 377
Query: 216 NKTVPPAERR--PTGQIVGIIKRKWRQYCGILQP---NPLAGSSRHLFVP-AERKIPKIR 269
+ + ++ PT ++V I +R WRQY G L P +P + S++++FV ++ +PK+R
Sbjct: 378 DAMIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCLPKVR 437
Query: 270 VETRQIATLSGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKF 329
+ TR+ A L +RIV++IDSWP +YP GHFVR LG I E E LLLEHDV + F
Sbjct: 438 IRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPF 497
Query: 330 SDLVLSYLPPMPWEKSTGRPWCSGTSI 356
S VL LP + G W + T +
Sbjct: 498 SKKVLECLP------AEGHDWKAPTKL 518
Score = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 35/72 (48%), Positives = 42/72 (58%)
Query: 402 LFQAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLL 461
+ A YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG + +
Sbjct: 815 MMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHR 874
Query: 462 DKKASTALCYNL 473
DK +C N+
Sbjct: 875 DKNKMDMICRNI 886
Score = 68.9 bits (167), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 42/134 (31%), Positives = 53/134 (39%), Gaps = 47/134 (35%)
Query: 476 DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLPGC 535
DF HYGLA IYTHFTSPIRRY D++ HR LA IG + + DK +C N
Sbjct: 830 DFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRN---- 885
Query: 536 TDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVA 595
+N ++R AQ+AGRAS+
Sbjct: 886 -------------------------------------------INRKHRNAQFAGRASIE 902
Query: 596 LHTHLFFRRKSITE 609
+ R TE
Sbjct: 903 YYVGQVMRNNESTE 916
Score = 59.7 bits (143), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 24/39 (61%), Positives = 30/39 (76%)
Query: 612 VARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
+ +R DLR +CS+DPPGC DI+DALH + LPNGN EV
Sbjct: 530 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEV 568
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/22 (72%), Positives = 18/22 (81%)
Query: 533 PGCTDIDDALHCRPLPNGNIEV 554
PGC DI+DALH + LPNGN EV
Sbjct: 547 PGCVDINDALHAKKLPNGNWEV 568
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 166 bits (420), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 96/271 (35%), Positives = 139/271 (51%), Gaps = 34/271 (12%)
Query: 114 DSLYPLHATPSEIHAGIKNQSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAI 173
D +P + + + + G+KN L QG+ Q S NFLEG V+ + KP+L+ G++ LNRA
Sbjct: 11 DFTFPEYYSTARVXGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAF 70
Query: 174 DGDTVAVRLLPESQWSAPXX----------------------XXXXXXXXXXXXXXXXXK 211
+GD V V LLP+S+W AP +
Sbjct: 71 NGDQVIVELLPQSEWKAPSSIVLDSEHFDVNDNPDIEAGDDDDNNESSSNTTVISDKQRR 130
Query: 212 LIKGNKTVPPAERR--PTGQIVGIIKRKWRQYCGILQP---NPLAGSSRHLFVPAERK-I 265
L+ + + ++ PT ++V I +R WRQY G L P +P + S++++FV K +
Sbjct: 131 LLAKDAXIAQRSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILXDKCL 190
Query: 266 PKIRVETRQIATLSGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVP 325
PK+R+ TR+ A L +RIV++IDSWP +YP GHFVR LG I E E LLLEHDV
Sbjct: 191 PKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVE 250
Query: 326 HSKFSDLVLSYLPPMPWEKSTGRPWCSGTSI 356
+ FS VL LP + G W + T +
Sbjct: 251 YRPFSKKVLECLP------AEGHDWKAPTKL 275
Score = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/69 (50%), Positives = 41/69 (59%)
Query: 405 AVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKK 464
A YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG + + DK
Sbjct: 575 AQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKN 634
Query: 465 ASTALCYNL 473
+C N+
Sbjct: 635 KXDXICRNI 643
Score = 68.2 bits (165), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/134 (31%), Positives = 53/134 (39%), Gaps = 47/134 (35%)
Query: 476 DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLPGC 535
DF HYGLA IYTHFTSPIRRY D++ HR LA IG + + DK +C N
Sbjct: 587 DFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKXDXICRN---- 642
Query: 536 TDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVA 595
+N ++R AQ+AGRAS+
Sbjct: 643 -------------------------------------------INRKHRNAQFAGRASIE 659
Query: 596 LHTHLFFRRKSITE 609
+ R TE
Sbjct: 660 YYVGQVXRNNESTE 673
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 24/39 (61%), Positives = 30/39 (76%)
Query: 612 VARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
+ +R DLR +CS+DPPGC DI+DALH + LPNGN EV
Sbjct: 287 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEV 325
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/22 (72%), Positives = 18/22 (81%)
Query: 533 PGCTDIDDALHCRPLPNGNIEV 554
PGC DI+DALH + LPNGN EV
Sbjct: 304 PGCVDINDALHAKKLPNGNWEV 325
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 459
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 503 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ 543
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 518
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 503 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ 543
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
R DL LD ++D D+DDAL + LP+ +++
Sbjct: 208 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQL 243
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 459
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 504 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ 544
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 518
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 504 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ 544
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
R DL LD ++D D++DAL + LP+ +++
Sbjct: 209 REDLTALDFVTIDSASTEDMNDALFAKALPDDKLQL 244
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii
pdb|2ID0|B Chain B, Escherichia Coli Rnase Ii
pdb|2ID0|C Chain C, Escherichia Coli Rnase Ii
pdb|2ID0|D Chain D, Escherichia Coli Rnase Ii
Length = 644
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYP-SLLDKKASTALCYNLPGCT 536
H+GL Y +TSPIR+Y D I HRLL A I G AT P + + + N
Sbjct: 484 HFGLGLEAYATWTSPIRKYGDXINHRLLKAVIKGETATRPQDEITVQXAERRRLNRXAER 543
Query: 537 DIDDALHCRPLPN 549
D+ D L+ R L +
Sbjct: 544 DVGDWLYARFLKD 556
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/41 (53%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 459
H+GL Y +TSPIR+Y D I HRLL A I G AT P
Sbjct: 484 HFGLGLEAYATWTSPIRKYGDXINHRLLKAVIKGETATRPQ 524
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
R DL LD ++D D DDAL + LP+ +++
Sbjct: 189 REDLTALDFVTIDSASTEDXDDALFAKALPDDKLQL 224
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|B Chain B, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|C Chain C, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7F|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Hexagonal Crystal Form.
Northeast Structural Genomics Target Drr63
Length = 469
Score = 35.8 bits (81), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%)
Query: 456 TYPSLLDKKASTALCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 511
T P+ ++ + A S H+G +Y TSP RRY D++VH+ L A +
Sbjct: 304 TLPAXWARRKTLARTRFQPSPGPHHGXGLDLYAQATSPXRRYLDLVVHQQLRAFLA 359
Score = 35.8 bits (81), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 413 LQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 452
Q S H+G +Y TSP RRY D++VH+ L A +
Sbjct: 320 FQPSPGPHHGXGLDLYAQATSPXRRYLDLVVHQQLRAFLA 359
>pdb|3MW3|A Chain A, Crystal Structure Of Beta-Neurexin 2 With The Splice
Insert 4
Length = 208
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 277 TLSGQRIVVAIDSWPRHSRYPQGHF 301
T SG + +DSWP + RYP G+F
Sbjct: 99 TRSGGNATLQVDSWPVNERYPAGNF 123
>pdb|3ASY|A Chain A, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASY|B Chain B, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|A Chain A, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|B Chain B, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
Length = 211
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 426 PIYTHFTSPIRRYADIIVHR 445
P++ HF P +RYAD+IV R
Sbjct: 167 PMHLHFVEPTKRYADVIVPR 186
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 485 PIYTHFTSPIRRYADIIVHR 504
P++ HF P +RYAD+IV R
Sbjct: 167 PMHLHFVEPTKRYADVIVPR 186
>pdb|2ZT9|C Chain C, Crystal Structure Of The Cytochrome B6f Complex From
Nostoc Sp. Pcc 7120
pdb|4H44|C Chain C, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
7120
Length = 289
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 28/119 (23%), Positives = 48/119 (40%), Gaps = 11/119 (9%)
Query: 286 AIDSWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKS 345
A ++P R P G V A + K TE EV P S D V + +P++ S
Sbjct: 5 AQQTYPETPREPTGRIVCANCHLAAKPTEVEV-------PQSVLPDTVFKAVVKIPYDTS 57
Query: 346 TGRPWCSGTSIGLSQISTGVISVGL----EQGFPSLLKPRTTFVFYDFPRTTRTNFILL 400
+ G+ +GL+ + ++ G E P LK V++ + N +++
Sbjct: 58 VQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEELKEEIGDVYFQPYGEDKDNIVIV 116
>pdb|1LJ2|A Chain A, Recognition Of Eif4g By Rotavirus Nsp3 Reveals A Basis For
Mrna Circularization
pdb|1LJ2|B Chain B, Recognition Of Eif4g By Rotavirus Nsp3 Reveals A Basis For
Mrna Circularization
Length = 110
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 71 RDLATQSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSLYPLHA 121
RDL + G LTSSIE Y+ ++ LD K + + + D++ PLHA
Sbjct: 27 RDLQNKIGSLTSSIEWYLRSME-----LDPEIKADIEQQINSIDAINPLHA 72
>pdb|1TU2|B Chain B, The Complex Of Nostoc Cytochrome F And Plastocyanin
Determin With Paramagnetic Nmr. Based On The Structures
Of Cytochrome F And Plastocyanin, 10 Structures
Length = 254
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/119 (23%), Positives = 48/119 (40%), Gaps = 11/119 (9%)
Query: 286 AIDSWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKS 345
A ++P R P G V A + K TE EV P S D V + +P++ S
Sbjct: 5 AQQTYPETPREPTGRIVCANCHLAAKPTEVEV-------PQSVLPDTVFKAVVKIPYDTS 57
Query: 346 TGRPWCSGTSIGLSQISTGVISVGL----EQGFPSLLKPRTTFVFYDFPRTTRTNFILL 400
+ G+ +GL+ + ++ G E P LK V++ + N +++
Sbjct: 58 VQQVGADGSKVGLNVGAVLMLPEGFKIAPEDRIPEELKEEIGDVYFQPYGEDKDNIVIV 116
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,713,045
Number of Sequences: 62578
Number of extensions: 805367
Number of successful extensions: 1789
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1738
Number of HSP's gapped (non-prelim): 50
length of query: 654
length of database: 14,973,337
effective HSP length: 105
effective length of query: 549
effective length of database: 8,402,647
effective search space: 4613053203
effective search space used: 4613053203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)