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= psy1904
(163 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5
Angstroms Resolution Reveals Structural Basis For Pax
Developmental Mutations
Length = 128
Score = 140 bits (354), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 65/88 (73%), Positives = 76/88 (86%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 29 MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 88
Query: 61 KTNPNITSWEVRDKLIKVSRLDDSDTES 88
+++P + SWE+R+KLI+ D S S
Sbjct: 89 RSSPGMFSWEIREKLIREGVCDRSTAPS 116
>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna
pdb|1K78|E Chain E, Pax5(1-149)+ets-1(331-440)+dna
pdb|1K78|I Chain I, Pax5(1-149)+ets-1(331-440)+dna
pdb|1MDM|A Chain A, Inhibited Fragment Of Ets-1 And Paired Domain Of Pax5
Bound To Dna
Length = 149
Score = 122 bits (307), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 58/86 (67%), Positives = 71/86 (82%), Gaps = 1/86 (1%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V ++I EYK
Sbjct: 44 LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103
Query: 61 KTNPNITSWEVRDKLIKVSRLDDSDT 86
+ NP + +WE+RD+L+ R+ D+DT
Sbjct: 104 RQNPTMFAWEIRDRLL-AERVCDNDT 128
>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain
Length = 159
Score = 120 bits (301), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 56/88 (63%), Positives = 68/88 (77%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A GVRPC ISRQLRVSHGCVSKIL RY ETGSIRPGVIGGSKP+VATP V ++I +YK
Sbjct: 37 LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYK 96
Query: 61 KTNPNITSWEVRDKLIKVSRLDDSDTES 88
+ NP + +WE+RD+L+ D+ S
Sbjct: 97 RQNPTMFAWEIRDRLLAEGVCDNDTVPS 124
>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna
Complex Reveals A General Model For Pax Protein-Dna
Interactions
Length = 133
Score = 103 bits (258), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 48/76 (63%), Positives = 61/76 (80%)
Query: 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60
+A +G RPC ISR L+VS+GCVSKIL RY TGSIRP IGGSKPRVATP+V +I +YK
Sbjct: 29 LAHSGARPCDISRILQVSNGCVSKILGRYYATGSIRPRAIGGSKPRVATPEVVSKIAQYK 88
Query: 61 KTNPNITSWEVRDKLI 76
+ P+I +WE+RD+L+
Sbjct: 89 QECPSIFAWEIRDRLL 104
>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 = 93.6 bits (231), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 46/80 (57%), Positives = 58/80 (72%)
Query: 82 DDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETR 141
D SD ESEPGI LKRKQRRSRTTF+++QL+ELE++F+R+ YPDIYTRE LA + +TE R
Sbjct: 2 DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61
Query: 142 VQQFVLGTAGFLLSCLPSVS 161
+Q + L SVS
Sbjct: 62 IQVWFQNRRARLRKQHTSVS 81
>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 = 79.0 bits (193), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 36/49 (73%), Positives = 42/49 (85%)
Query: 95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
KRKQRR RTTFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 51
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 73.6 bits (179), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 33/46 (71%), Positives = 40/46 (86%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
QRRSRTTFT+ QLEELE++F+R+HYPDIYTRE LA + +TE RVQ
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQ 47
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 70.1 bits (170), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 31/44 (70%), Positives = 37/44 (84%)
Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
R RTTFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 69.7 bits (169), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 32/47 (68%), Positives = 39/47 (82%)
Query: 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
K+RR+RTTFTS QLEELEK FQ++HYPD+Y RE LA + +TE RVQ
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQ 54
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 29/43 (67%), Positives = 35/43 (81%)
Query: 101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
S TFTS QLEELEK+F R+HYPD++TRE LA K G+TE R+Q
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 59.3 bits (142), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 28/45 (62%), Positives = 34/45 (75%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
QRR RT FTS QL+ELE +FQR+HYPD+ TRE +A +TE RV
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARV 47
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/44 (54%), Positives = 33/44 (75%)
Query: 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
R+RT+FT Q+E LEK F+R+HYPD++ RE LA K + E R+Q
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/45 (60%), Positives = 33/45 (73%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
QRR RT FTS QL+ELE +FQR+ YPD+ TRE +A +TE RV
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARV 47
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/45 (55%), Positives = 32/45 (71%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RTTFT AQL+ LE F ++ YPDI+ RE +A K + E+RVQ
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 29/45 (64%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RT FT QLE LE FQ + YPD+ TRE LA K + E +V+
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 89 EPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQF 145
EPG K K RRSRT FT QL LEK F++ Y R LA G+++ +V+ +
Sbjct: 9 EPGTKAK-KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTW 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
K RR RT FTS QL ELEK F Y + R +A+ ++E +V+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVK 52
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RT FT Q+E LE F+ + YP I E LA K + R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 29/45 (64%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
R+ RT ++S QL L++ FQ++ Y + R LA G+T+T+V+
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVK 52
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
R+ RT FT+AQL LE+ F++ Y I R ++ +TET+V+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45
>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 = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFV 146
K+++ RT+FT Q+ ELEK F + Y R ALA MT+ +V+ +
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWF 65
>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 = 33.5 bits (75), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
L K+R+ R FT AQ ELE+ F++ Y RE LA+ +T T+V+
Sbjct: 5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR R T+T Q ELEK F +HY R +A+ +TE +++
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIK 65
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 19/24 (79%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHY 122
RR+RTTFTS+Q+ ELE+ F + Y
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRY 26
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
+R RT+F QL ++ F +H PD + LA K G+T+ +Q
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 31.6 bits (70), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
L K+R+ R FT AQ ELE+ F++ Y RE L + +T T+V+
Sbjct: 8 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVK 57
>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 = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
+R+RT +T AQL ELEK F + Y R LA +TE ++
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIK 48
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 103 TTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFV 146
T+F+ +Q+ ELE+ F R Y R ALA MT+ +V+ +
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWF 45
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 30.4 bits (67), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 102 RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RT FT+ QL ELEK F + Y R +A + ET+V+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 79
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRV 142
K++++RT F+S QL L FQR Y + + L+N ++ +V
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
>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 = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 24/45 (53%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
RR RT FT QL LEK F + +Y R LA + + E+ ++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK 46
>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 = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
+R RT++T Q ELEK F + Y R +A+ +TE +++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73
>pdb|1FNM|A Chain A, Structure Of Thermus Thermophilus Ef-G H573a
pdb|1PN6|A Chain A, Domain-Wise Fitting Of The Crystal Structure Of
T.Thermophilus Ef-G Into The Low Resolution Map Of The
Release Complex.Puromycin.Efg.Gdpnp Of E.Coli 70s
Ribosome
Length = 691
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 39 VIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESE 89
++GG P+ P V+K IEE ++ P I + V D IKV+ D S E +
Sbjct: 529 IVGGVIPKEYIPAVQKGIEEAMQSGPLI-GFPVVD--IKVTLYDGSYAEVD 576
>pdb|1ZN0|B Chain B, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The
50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf
Length = 655
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 38 GVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESE 89
++GG P+ P V+K IEE ++ P I + V D IKV+ D S E +
Sbjct: 495 AIVGGVIPKEYIPAVQKGIEEAMQSGPLI-GFPVVD--IKVTLYDGSYAEVD 543
>pdb|3IZP|E Chain E, Conformation Of Ef-G During Translocation
Length = 688
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 39 VIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLDDSDTESE 89
++GG P+ P V+K IEE ++ P I + V D IKV+ D S E +
Sbjct: 529 IVGGVIPKEYIPAVQKGIEEAMQSGPLI-GFPVVD--IKVTLYDGSYAEVD 576
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
+R+R T+T Q ELEK F + Y R +AN ++E +++
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIK 48
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using A
Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 26.6 bits (57), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
++R R T+T Q ELEK F + Y R +A+ +TE +++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 47
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 26.2 bits (56), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQ 143
++R R T+T Q ELEK F + Y R +A+ +TE +++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 47
>pdb|2CKJ|A Chain A, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|B Chain B, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|C Chain C, Human Milk Xanthine Oxidoreductase
pdb|2CKJ|D Chain D, Human Milk Xanthine Oxidoreductase
Length = 1333
Score = 26.2 bits (56), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 40 IGGSKPRVATPDVEKRIEEYKKTNPNITSWE 70
+ G A + KR+E YKK NP+ SWE
Sbjct: 1086 LNGQAVYAACQTILKRLEPYKKKNPS-GSWE 1115
>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor
(Nnrti)
Length = 557
Score = 26.2 bits (56), Expect = 9.7, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 28 RYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLD 82
RYQ ++ P GS P ++ + K +E +KK NP+I ++ D L S L+
Sbjct: 145 RYQY--NVLPQGWKGS-PAISQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLE 196
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
Length = 556
Score = 26.2 bits (56), Expect = 9.7, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 28 RYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLD 82
RYQ ++ P GS P ++ + K +E +KK NP+I ++ D L S L+
Sbjct: 144 RYQY--NVLPQGWKGS-PAISQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLE 195
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
Length = 555
Score = 26.2 bits (56), Expect = 9.9, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 28 RYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSRLD 82
RYQ ++ P GS P ++ + K +E +KK NP+I ++ D L S L+
Sbjct: 143 RYQY--NVLPQGWKGS-PAISQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLE 194
>pdb|2E1Q|A Chain A, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|B Chain B, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|C Chain C, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
pdb|2E1Q|D Chain D, Crystal Structure Of Human Xanthine Oxidoreductase Mutant,
Glu803val
Length = 1333
Score = 26.2 bits (56), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 40 IGGSKPRVATPDVEKRIEEYKKTNPNITSWE 70
+ G A + KR+E YKK NP+ SWE
Sbjct: 1086 LNGQAVYAACQTILKRLEPYKKKNPS-GSWE 1115
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
0.317 0.132 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,567,121
Number of Sequences: 62578
Number of extensions: 168159
Number of successful extensions: 531
Number of sequences better than 100.0: 61
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 485
Number of HSP's gapped (non-prelim): 61
length of query: 163
length of database: 14,973,337
effective HSP length: 91
effective length of query: 72
effective length of database: 9,278,739
effective search space: 668069208
effective search space used: 668069208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)