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= psy15107
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 91.7 bits (226), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 43/47 (91%), Positives = 45/47 (95%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RRERTTFTRAQLDVLE+LF KTRYPDIFMREEVALKINLPESRVQ +
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVW 54
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/50 (60%), Positives = 38/50 (76%)
Query: 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RKQRR RTTFT QL+ LE F +T YPD+F REE+A+KI L E+R+Q +
Sbjct: 4 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVW 53
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/50 (58%), Positives = 39/50 (78%)
Query: 66 RKQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RKQRR RTTF+ +QLD LE F +T+YPDI+ REE+A + NL E+R+Q +
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVW 65
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/49 (53%), Positives = 38/49 (77%)
Query: 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
K+RR RTTFT QL+ LE +F KT YPD++ RE++A++ +L E+RVQ +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVW 56
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 35/46 (76%)
Query: 70 RERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
R RT+FT+ Q++ LE F +T YPD+F RE +A KI+LPE+R+Q +
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVW 54
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 34/46 (73%)
Query: 70 RERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
R RTTFT QL+ LE F +T YPD+F REE+A+KI L E+R+Q +
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVW 46
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/48 (56%), Positives = 34/48 (70%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
QRR RTTFT QL+ LE F +T YPDI+ REE+A + L E+RVQ +
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVW 49
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/48 (52%), Positives = 34/48 (70%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
QRR+RT FT QL LE+ F + RYPD+ REE+A+ NL E+RV+ +
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVW 50
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 23/42 (54%), Positives = 31/42 (73%)
Query: 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
TFT QL+ LE F +T YPD+F REE+A+KI L E+R+Q +
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVW 46
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 23/47 (48%), Positives = 35/47 (74%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RR RT FT QL+ LE+LF +T+YPD+ RE++A K++L E +V+ +
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVW 54
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 33/48 (68%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
QRR+RT FT QL LE+ F + YPD+ REE+A+ NL E+RV+ +
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVW 50
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKI 128
RR RT FT+ Q++VLE++F YP I + E++A K+NL R+Q + F LK
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIW---FQNRRAKLKR 58
Query: 129 NLPESTF 135
+ ES F
Sbjct: 59 SHRESQF 65
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 28/47 (59%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RR RT FTR QL LE F K Y R E+A ++NLPES ++ +
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVW 48
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 74 TFTRAQLDVLESLFGKTRYPDIFMREEVALKIN 106
T+ + L V+ES F + +YPD REE+A N
Sbjct: 13 TWRKECLAVMESYFNENQYPDEAKREEIANACN 45
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
++R RT F+ QL L+ F + RY R++++ ++ L E++V+G+
Sbjct: 4 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGW 51
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
Length = 63
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
+R RT +TRAQL LE F +Y R E+A+ +NL E ++ +
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIW 50
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 72 RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RT F++AQL L+ F K +Y + +E++ +NL +V+ +
Sbjct: 7 RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTW 50
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 29.6 bits (65), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113
K+R+ R FT+AQ LE F + RY RE +A I L ++V+
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54
>pdb|3AC0|A Chain A, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|B Chain B, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|C Chain C, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|D Chain D, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
Length = 845
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 23 TSCGGGGAAMASYLKSAPYG--VNGIGLSMDSL-----HSSLG 58
TS GGG A+M SY +PY VN +G +D H S+G
Sbjct: 350 TSSGGGSASMNSYYVVSPYEGIVNKLGKEVDYTVGAYSHKSIG 392
>pdb|3MCU|A Chain A, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215.
pdb|3MCU|B Chain B, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215.
pdb|3MCU|C Chain C, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215.
pdb|3MCU|D Chain D, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215.
pdb|3MCU|E Chain E, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215.
pdb|3MCU|F Chain F, Crystal Structure Of The Dipicolinate Synthase Chain B
From Bacillus Cereus. Northeast Structural Genomics
Consortium Target Bcr215
Length = 207
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 42 GVNGIGLSMDSLHSSLGYIPSGNHRKQRRERTTFTRAQL---DVLESLFGKTRYPDIFMR 98
G+NG+ L ++ ++P G +++ + R +L VLE+L GK P + +
Sbjct: 135 GLNGVNLXRLXATKNIYFVPFGQDAPEKKPNSXVARXELLEDTVLEALQGKQLQPVVVEK 194
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
+R+RT++TR Q LE F RY R E+A ++L E +++ +
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIW 75
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQ 113
K+R+ R FT+AQ LE F + RY RE + I L ++V+
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVK 57
>pdb|3KS7|A Chain A, Crystal Structure Of Putative Peptide:n-Glycosidase F
(Pngase F) (Yp_210507.1) From Bacteroides Fragilis Nctc
9343 At 2.30 A Resolution
pdb|3KS7|B Chain B, Crystal Structure Of Putative Peptide:n-Glycosidase F
(Pngase F) (Yp_210507.1) From Bacteroides Fragilis Nctc
9343 At 2.30 A Resolution
pdb|3KS7|C Chain C, Crystal Structure Of Putative Peptide:n-Glycosidase F
(Pngase F) (Yp_210507.1) From Bacteroides Fragilis Nctc
9343 At 2.30 A Resolution
pdb|3KS7|D Chain D, Crystal Structure Of Putative Peptide:n-Glycosidase F
(Pngase F) (Yp_210507.1) From Bacteroides Fragilis Nctc
9343 At 2.30 A Resolution
Length = 397
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 75 FTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALKINLPE 132
A +DV ES D+ + V N Q YPDIF R +V+ +P+
Sbjct: 200 LVNADIDVKESRLAC----DVLPKRHVEPLXNTVYYXGQSYPDIFARRDVSTDFTVPK 253
>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
Saccharomyces Cerevisiae, Form Spt6(239-1451)
Length = 1219
Score = 28.1 bits (61), Expect = 1.7, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 48 LSMDSLHSSLGYIPSGNHRKQRRERTTFTRAQL-DVLESLFGKTRYPDIFMREEVALKIN 106
L++D++ S N + + + R+ F++ L DV+ + GK + E++ IN
Sbjct: 337 LAIDTVQKYYSLELSKNTKIREKVRSDFSKYYLADVVLTAKGKKEIQKGSLYEDIKYAIN 396
Query: 107 LPESRVQGYPDIFMREEVALKINL 130
+ PD+F++ A +NL
Sbjct: 397 RTPMHFRRDPDVFLKMVEAESLNL 420
>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
Saccharomyces Cerevisiae, Form Spt6(236-1259)
Length = 1030
Score = 28.1 bits (61), Expect = 1.7, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 48 LSMDSLHSSLGYIPSGNHRKQRRERTTFTRAQL-DVLESLFGKTRYPDIFMREEVALKIN 106
L++D++ S N + + + R+ F++ L DV+ + GK + E++ IN
Sbjct: 340 LAIDTVQKYYSLELSKNTKIREKVRSDFSKYYLADVVLTAKGKKEIQKGSLYEDIKYAIN 399
Query: 107 LPESRVQGYPDIFMREEVALKINL 130
+ PD+F++ A +NL
Sbjct: 400 RTPMHFRRDPDVFLKMVEAESLNL 423
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
K+++ RT F+ QL VL F + +Y + +E++ +NL +V+ +
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTW 69
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 93
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 67 KQRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
K+++ RT+FTR Q+ LE F K +Y R +A + + +++V+ +
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTW 64
>pdb|1EU8|A Chain A, Structure Of Trehalose Maltose Binding Protein From
Thermococcus Litoralis
Length = 409
Score = 26.9 bits (58), Expect = 3.5, Method: Composition-based stats.
Identities = 10/31 (32%), Positives = 21/31 (67%)
Query: 69 RRERTTFTRAQLDVLESLFGKTRYPDIFMRE 99
+R+ T + +LD++ +L GK+ PD+F+ +
Sbjct: 39 KRQATDTEQRRLDLVNALRGKSSDPDVFLMD 69
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 72 RTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
RT FT QL LE F +Y R E+A + L E++V+ +
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIW 81
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 73 TTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLP 108
T FT QL VL+ F YP E+++ +NLP
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLP 47
>pdb|3EEY|A Chain A, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|B Chain B, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|C Chain C, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|D Chain D, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|E Chain E, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|F Chain F, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|G Chain G, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|H Chain H, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|I Chain I, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
pdb|3EEY|J Chain J, Crystal Structure Of Putative Rrna-Methylase From
Clostridium Thermocellum
Length = 197
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 56 SLGYIPSGNHRKQRRERTTF 75
+LGY+PSG+H R TT
Sbjct: 100 NLGYLPSGDHSISTRPETTI 119
>pdb|4B4F|A Chain A, Thermobifida Fusca Cel6b(e3) Co-crystallized With
Cellobiose
pdb|4B4F|B Chain B, Thermobifida Fusca Cel6b(e3) Co-crystallized With
Cellobiose
pdb|4B4H|A Chain A, Thermobifida Fusca Cellobiohydrolase Cel6b(e3) Catalytic
Domain
pdb|4B4H|B Chain B, Thermobifida Fusca Cellobiohydrolase Cel6b(e3) Catalytic
Domain
Length = 420
Score = 25.8 bits (55), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 17 AFPSFGTSCGG-GGAAMASYLKSAPYGVNGIGLSMDSLHSSLGYIPS 62
+ P+ T+ GG GG + +Y+K VNG+G ++ LG IP+
Sbjct: 137 SLPNLVTNVGGNGGTELCAYMKQNGGYVNGVGYAL----RKLGEIPN 179
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGYPDIFMREEVALK 127
++R RT F+ QL L+ F + RY R++++ ++ L E++++ + F E +K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIW---FQNERAKIK 57
>pdb|2QW5|A Chain A, Crystal Structure Of A Putative Sugar Phosphate
IsomeraseEPIMERASE (Ava4194) From Anabaena Variabilis
Atcc 29413 At 1.78 A Resolution
pdb|2QW5|B Chain B, Crystal Structure Of A Putative Sugar Phosphate
IsomeraseEPIMERASE (Ava4194) From Anabaena Variabilis
Atcc 29413 At 1.78 A Resolution
Length = 335
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 32 MASYLKSAPYGVNGIGLSMDSLHSSLGYIPSGNHRKQRRERTTFTRAQLDVLESLFGK 89
+ YL S G+ + +S + + ++ + PS N+ +QR+E + ++++D+ +L G+
Sbjct: 70 LRHYLDSE--GLENVKISTN-VGATRTFDPSSNYPEQRQEALEYLKSRVDITAALGGE 124
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
++R RT F+ QL L+ F + RY R++++ ++ L E++++ +
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIW 50
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 25.4 bits (54), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 68 QRRERTTFTRAQLDVLESLFGKTRYPDIFMREEVALKINLPESRVQGY 115
++R RT F+ QL L+ F + RY R++++ ++ L E++++ +
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIW 48
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
0.318 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,176,477
Number of Sequences: 62578
Number of extensions: 158986
Number of successful extensions: 803
Number of sequences better than 100.0: 71
Number of HSP's better than 100.0 without gapping: 53
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 732
Number of HSP's gapped (non-prelim): 87
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)