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= psy2181
(490 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 88.2 bits (217), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 43/51 (84%), Positives = 45/51 (88%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
QRNRTSFT EQI++LEKEFERTHYPDVFARERLA KI LPEARIQV NR
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/35 (85%), Positives = 30/35 (85%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQVSSINR 261
KEFERTHYPDVFARERLA KI LPEARIQV NR
Sbjct: 24 KEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/22 (100%), Positives = 22/22 (100%)
Query: 339 QVWFSNRRAKWRREEKLRNQRR 360
QVWFSNRRAKWRREEKLRNQRR
Sbjct: 52 QVWFSNRRAKWRREEKLRNQRR 73
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/50 (68%), Positives = 38/50 (76%)
Query: 109 RNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
R RT+FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/35 (74%), Positives = 26/35 (74%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQVSSINR 261
K F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 16 KAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 316 HNPGSVTPISRDDAKGLVQQSARQVWFSNRRAKWRREE 353
H P T GL + QVWF NRRAKWR++E
Sbjct: 22 HYPDVFTREELAMKIGLTEARI-QVWFQNRRAKWRKQE 58
>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 = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/51 (66%), Positives = 39/51 (76%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R RT+FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 57
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/35 (74%), Positives = 26/35 (74%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQVSSINR 261
K F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 23 KAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 57
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/17 (76%), Positives = 16/17 (94%)
Query: 339 QVWFSNRRAKWRREEKL 355
QVWF NRRAKWR++EK+
Sbjct: 51 QVWFQNRRAKWRKQEKV 67
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/51 (58%), Positives = 41/51 (80%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+RNRT+FT+ Q++ LEK F++THYPDV+ARE+LA + L EAR+QV NR
Sbjct: 10 RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/35 (60%), Positives = 27/35 (77%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQVSSINR 261
K F++THYPDV+ARE+LA + L EAR+QV NR
Sbjct: 26 KVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 339 QVWFSNRRAKWRREEKL 355
QVWF NRRAKWR+ E+
Sbjct: 54 QVWFQNRRAKWRKRERF 70
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 65.9 bits (159), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 30/54 (55%), Positives = 40/54 (74%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 161
+R+RT+FT EQ++ LE+ FERTHYPD++ RE LA + L EAR+QV NR R
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 25/36 (69%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 264
FERTHYPD++ RE LA + L EAR+QV NR R
Sbjct: 21 FERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 14/14 (100%)
Query: 339 QVWFSNRRAKWRRE 352
QVWFSNRRA+WR++
Sbjct: 47 QVWFSNRRARWRKQ 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 65.1 bits (157), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 31/46 (67%), Positives = 35/46 (76%)
Query: 113 SFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/35 (74%), Positives = 26/35 (74%)
Query: 227 KEFERTHYPDVFARERLADKIGLPEARIQVSSINR 261
K F RTHYPDVF RE LA KIGL EARIQV NR
Sbjct: 16 KAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 13/17 (76%), Positives = 16/17 (94%)
Query: 339 QVWFSNRRAKWRREEKL 355
QVWF NRRAKWR++EK+
Sbjct: 44 QVWFQNRRAKWRKQEKV 60
>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 = 62.4 bits (150), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 35/82 (42%), Positives = 45/82 (54%), Gaps = 10/82 (12%)
Query: 80 ESTSDINSEPNSSADEDSQMXXXXXXXXQRNRTSFTNEQIDSLEKEFERTHYPDVFARER 139
E SD SEP + +R+RT+F+ Q+D LE+ FERT YPD++ RE
Sbjct: 1 EDISDCESEPGIAL----------KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREE 50
Query: 140 LADKIGLPEARIQVSSINRVLR 161
LA + L EARIQV NR R
Sbjct: 51 LAQRTNLTEARIQVWFQNRRAR 72
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 24/36 (66%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 264
FERT YPD++ RE LA + L EARIQV NR R
Sbjct: 37 FERTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR 72
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/51 (54%), Positives = 36/51 (70%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R RT+FT Q+D LE F +T YPD+F RE +A KI LPE+R+QV NR
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/33 (57%), Positives = 24/33 (72%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINR 261
F +T YPD+F RE +A KI LPE+R+QV NR
Sbjct: 26 FAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 37/51 (72%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R+RT FT+EQ+++LE F+ T YPDV RE+LA K+ L E +++V NR
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINR 261
F+ T YPDV RE+LA K+ L E +++V NR
Sbjct: 26 FQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/13 (84%), Positives = 12/13 (92%)
Query: 339 QVWFSNRRAKWRR 351
+VWF NRRAKWRR
Sbjct: 52 EVWFKNRRAKWRR 64
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R RT FT++Q+ LE F+R HYPD+ RE +A L EAR++V NR
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNR 54
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINR 261
F+R HYPD+ RE +A L EAR++V NR
Sbjct: 22 FQRNHYPDMSTREEIAVWTNLTEARVRVWFKNR 54
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 339 QVWFSNRRAKWRREEKL 355
+VWF NRRAKWR+ E+
Sbjct: 48 RVWFKNRRAKWRKREEF 64
>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 = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R RT FT++Q+ LE F+R YPD+ RE +A L EAR++V NR
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 54
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 229 FERTHYPDVFARERLADKIGLPEARIQVSSINR 261
F+R YPD+ RE +A L EAR++V NR
Sbjct: 22 FQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 54
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 339 QVWFSNRRAKWRREEKL 355
+VWF NRRAKWR+ E+
Sbjct: 48 RVWFKNRRAKWRKREEF 64
>pdb|1GIQ|A Chain A, Crystal Structure Of The Enzymatic Componet Of Iota-Toxin
From Clostridium Perfringens With Nadh
pdb|1GIQ|B Chain B, Crystal Structure Of The Enzymatic Componet Of Iota-Toxin
From Clostridium Perfringens With Nadh
pdb|1GIR|A Chain A, Crystal Structure Of The Enzymatic Componet Of Iota-Toxin
From Clostridium Perfringens With Nadph
pdb|3BUZ|A Chain A, Crystal Structure Of Ia-Btad-Actin Complex
Length = 413
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 269 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 324
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 111 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 170
Query: 325 SRDDAKGLVQQ 335
+ +D K L++Q
Sbjct: 171 NSNDVKTLIEQ 181
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGL-----PEARIQVSSINRVLRNLAA 165
R F + QI+S +E E + + ++ ++ I + PE + N+ +R
Sbjct: 56 RQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEK----FAFNKEIRT-EN 110
Query: 166 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 221
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 111 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 170
Query: 222 SRDDAKEFERTHY 234
+ +D K Y
Sbjct: 171 NSNDVKTLIEQDY 183
>pdb|4GY2|A Chain A, Crystal Structure Of Apo-ia-actin Complex
pdb|4H03|A Chain A, Crystal Structure Of Nad+-ia-actin Complex
pdb|4H0T|A Chain A, Crystal Structure Of Ia-adpr-actin Complex
Length = 418
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 269 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 324
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 325 SRDDAKGLVQQ 335
+ +D K L++Q
Sbjct: 176 NSNDVKTLIEQ 186
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGL-----PEARIQVSSINRVLRNLAA 165
R F + QI+S +E E + + ++ ++ I + PE + N+ +R
Sbjct: 61 RQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEK----FAFNKEIRT-EN 115
Query: 166 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 221
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 222 SRDDAKEFERTHY 234
+ +D K Y
Sbjct: 176 NSNDVKTLIEQDY 188
>pdb|4H0Y|A Chain A, Crystal Structure Of Nad+-ia(e380s)-actin Complex
Length = 418
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 269 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 324
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 325 SRDDAKGLVQQ 335
+ +D K L++Q
Sbjct: 176 NSNDVKTLIEQ 186
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGL-----PEARIQVSSINRVLRNLAA 165
R F + QI+S +E E + + ++ ++ I + PE + N+ +R
Sbjct: 61 RQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEK----FAFNKEIRT-EN 115
Query: 166 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 221
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 222 SRDDAKEFERTHY 234
+ +D K Y
Sbjct: 176 NSNDVKTLIEQDY 188
>pdb|4H0V|A Chain A, Crystal Structure Of Nad+-ia(e378s)-actin Complex
Length = 418
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 269 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 324
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 325 SRDDAKGLVQQ 335
+ +D K L++Q
Sbjct: 176 NSNDVKTLIEQ 186
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGL-----PEARIQVSSINRVLRNLAA 165
R F + QI+S +E E + + ++ ++ I + PE + N+ +R
Sbjct: 61 RQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEK----FAFNKEIRT-EN 115
Query: 166 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 221
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 222 SRDDAKEFERTHY 234
+ +D K Y
Sbjct: 176 NSNDVKTLIEQDY 188
>pdb|4H0X|A Chain A, Crystal Structure Of Nad+-ia(e380a)-actin Complex
Length = 418
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 269 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 324
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 325 SRDDAKGLVQQ 335
+ +D K L++Q
Sbjct: 176 NSNDVKTLIEQ 186
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGL-----PEARIQVSSINRVLRNLAA 165
R F + QI+S +E E + + ++ ++ I + PE + N+ +R
Sbjct: 61 RQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEK----FAFNKEIRT-EN 115
Query: 166 QKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLALPHNPGSVTPI 221
Q E N+ ET+ DKL +G + Y PG+ PTP HL LP N G + I
Sbjct: 116 QNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYI 175
Query: 222 SRDDAKEFERTHY 234
+ +D K Y
Sbjct: 176 NSNDVKTLIEQDY 188
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 33/63 (52%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLRNLAAQK 167
+R RT+FT QI+ LE F YP + E LA K+ L RIQ+ NR + + +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 168 EQQ 170
E Q
Sbjct: 62 ESQ 64
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 35/55 (63%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLRN 162
+R RT+FT +Q+ LEKEF + +Y R LA ++ LPE+ I+V NR +++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKD 56
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 161
+R+RT FT Q+ LEK FE+ Y R LA+ +GL + +++ NR ++
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
>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 = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 32/46 (69%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 47
>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 = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 32/46 (69%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|2WN6|A Chain A, Structural Basis For Substrate Recognition In The
Enzymatic Component Of Adp-Ribosyltransferase Toxin Cdta
From Clostridium Difficile
Length = 463
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 5/82 (6%)
Query: 258 SINRVLRNLAAQKEQQASAHNQTSETVYDKLRMFNGQPGWA-WYPGS---TPTPSPAHLA 313
+ N+V+R Q E N+ ET+ +KL +G + W PG PTP HL
Sbjct: 151 AFNKVIRT-ENQNEISLEKFNEFKETIQNKLFKQDGFKDISLWEPGKGDEKPTPLLMHLK 209
Query: 314 LPHNPGSVTPISRDDAKGLVQQ 335
LP N G + + ++ L++Q
Sbjct: 210 LPRNTGMLPYTNTNNVSTLIEQ 231
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 155 SINRVLRNLAAQKEQQASAHNQTSETVYDKLRMFNGQPGWA-WYPGS---TPTPSPAHLA 210
+ N+V+R Q E N+ ET+ +KL +G + W PG PTP HL
Sbjct: 151 AFNKVIRT-ENQNEISLEKFNEFKETIQNKLFKQDGFKDISLWEPGKGDEKPTPLLMHLK 209
Query: 211 LPHNPGSV 218
LP N G +
Sbjct: 210 LPRNTGML 217
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 37.0 bits (84), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 32/46 (69%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 47
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 32/46 (69%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 30/43 (69%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 45
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 36.6 bits (83), Expect = 0.031, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 31/51 (60%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
+R RT+FT+EQ+ LEKEF Y + R ++A + L E ++++ NR
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNR 58
Score = 28.5 bits (62), Expect = 8.9, Method: Composition-based stats.
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 339 QVWFSNRRAKWRR 351
++WF NRRAKW+R
Sbjct: 52 KIWFQNRRAKWKR 64
>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 = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 32/46 (69%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 47
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 36.6 bits (83), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 30/43 (69%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
RT+F++EQ+ L++EF Y R++L+ ++GL EA+I++
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 45
>pdb|2WN4|A Chain A, Structural Basis For Substrate Recognition In The
Enzymatic Component Of Adp-Ribosyltransferase Toxin Cdta
From Clostridium Difficile
pdb|2WN5|A Chain A, Structural Basis For Substrate Recognition In The
Enzymatic Component Of Adp-Ribosyltransferase Toxin Cdta
From Clostridium Difficile
pdb|2WN7|A Chain A, Structural Basis For Substrate Recognition In The
Enzymatic Component Of Adp-Ribosyltransferase Toxin Cdta
From Clostridium Difficile
pdb|2WN8|A Chain A, Structural Basis For Substrate Recognition In The
Enzymatic Component Of Adp-Ribosyltransferase Toxin Cdta
From Clostridium Difficile
Length = 463
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 5/82 (6%)
Query: 258 SINRVLRNLAAQKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLA 313
+ N+V+R Q E N+ ET+ +KL +G + Y PG PTP HL
Sbjct: 151 AFNKVIRT-ENQNEISLEKFNEFKETIQNKLFKQDGFKDISLYEPGKGDEKPTPLLMHLK 209
Query: 314 LPHNPGSVTPISRDDAKGLVQQ 335
LP N G + + ++ L++Q
Sbjct: 210 LPRNTGMLPYTNTNNVSTLIEQ 231
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 155 SINRVLRNLAAQKEQQASAHNQTSETVYDKLRMFNGQPGWAWY-PGS---TPTPSPAHLA 210
+ N+V+R Q E N+ ET+ +KL +G + Y PG PTP HL
Sbjct: 151 AFNKVIRT-ENQNEISLEKFNEFKETIQNKLFKQDGFKDISLYEPGKGDEKPTPLLMHLK 209
Query: 211 LPHNPGSV 218
LP N G +
Sbjct: 210 LPRNTGML 217
>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 = 35.0 bits (79), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 31/45 (68%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQ 152
+R RT+F++EQ+ L++EF Y R++L+ ++GL EA+++
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVK 49
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.0 bits (79), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RTSF + Q+ +++ F H PD ++LA K GL + +QV
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQV 53
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 11/47 (23%)
Query: 310 AHLALPHNPGSVTPISRDDAKGLVQQSAR-----QVWFSNRRAKWRR 351
++ A+ HNP + D K L Q++ QVWF N RAK+RR
Sbjct: 24 SYFAINHNPDA------KDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 321 VTPISRDDAKGLVQQSARQV--WFSNRRAKWRR 351
++P R ++Q S RQV WF NRRAKWRR
Sbjct: 32 LSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 114 FTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
F+N+Q LEK+FE Y R+RLA + L E +++ NR
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNR 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 31/46 (67%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
+R RT+F++EQ+ ++EF Y R++L+ ++GL EA+I++
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLRNLAAQK 167
+R R ++T Q LEKEF HY R +A + L E +I++ N R + +K
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN---RRMKLKK 77
Query: 168 EQQA 171
E QA
Sbjct: 78 EIQA 81
>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 = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 128 RTHYPDVFA---RERLADKIGLPEARI-QVSSINRVLRNLAAQKEQ 169
+ P +FA R+RL + I VSSINRVLRNLA++K+Q
Sbjct: 88 KQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEKQQ 133
Score = 32.7 bits (73), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 231 RTHYPDVFA---RERLADKIGLPEARI-QVSSINRVLRNLAAQKEQ 272
+ P +FA R+RL + I VSSINRVLRNLA++K+Q
Sbjct: 88 KQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEKQQ 133
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/17 (82%), Positives = 17/17 (100%)
Query: 3 VSSINRVLRNLAAQKEQ 19
VSSINRVLRNLA++K+Q
Sbjct: 117 VSSINRVLRNLASEKQQ 133
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 28/43 (65%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQV 153
RT +++ Q+ +L++ F++T Y + R LA +GL + ++++
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKI 53
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLRNLAAQKE 168
RT+FT Q+ LEKEF Y R +A + L E ++++ NR ++ ++E
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>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 = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 161
+R RTS+T Q LEKEF Y R +A + L E +I++ NR ++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 339 QVWFSNRRAKWRREEK 354
++WF NRR KW++E K
Sbjct: 73 KIWFQNRRMKWKKEHK 88
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINR 158
RT FT Q+ +LE++F + Y + R + + L E ++++ NR
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNR 51
>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 = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 111 RTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVL---RNLAAQK 167
RTSFT Q+ LEK F + Y R LA + + +A+++ NR R A ++
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER 80
Query: 168 EQQASAHNQ 176
E + A N+
Sbjct: 81 EAERQAANR 89
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 329 AKGLVQQSAR-QVWFSNRRAKWRRE 352
A+GL A+ + WF NRR KWRR+
Sbjct: 51 ARGLKMTDAQVKTWFQNRRTKWRRQ 75
>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 = 2.3, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLR 161
+R RT++T Q+ LEKEF Y R LA + L E I++ NR ++
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
Score = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 339 QVWFSNRRAKWRREE 353
++WF NRR KW++EE
Sbjct: 48 KIWFQNRRMKWKKEE 62
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLAD---KIGLPEARIQVSSINRVLRN 162
+R RT+FT+ QI LE+ F + Y RLAD K+ L A++++ NR R+
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRY---LTAPRLADLSAKLALGTAQVKIWFKNRRRRH 57
>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 = 30.0 bits (66), Expect = 3.2, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 339 QVWFSNRRAKWRREEKLRNQ 358
++WF NRR KW++E K + +
Sbjct: 47 KIWFQNRRMKWKKENKTKGE 66
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity With
The Intact Antennapedia Homeodomain
Length = 62
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 339 QVWFSNRRAKWRREEKLRNQ 358
++WF NRR KW++E K + +
Sbjct: 41 KIWFQNRRMKWKKENKTKGE 60
>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 = 29.3 bits (64), Expect = 5.3, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 339 QVWFSNRRAKWRREEKLRNQ 358
++WF NRR KW++E K + +
Sbjct: 47 KIWFQNRRMKWKKENKTKGE 66
>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 = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 29/67 (43%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQVSSINRVLRNLAAQK 167
++ R FT Q LE+ F + Y RE LA I L ++++ N + AQ
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN 69
Query: 168 EQQASAH 174
E+ H
Sbjct: 70 EKGYEGH 76
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 108 QRNRTSFTNEQIDSLEKEFERTHYPDVFARERLADKIGLPEARIQ 152
+R RT T++Q+ L + F+ + P + +ADK GLP+ I+
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
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
0.312 0.126 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,318,632
Number of Sequences: 62578
Number of extensions: 433198
Number of successful extensions: 1059
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 935
Number of HSP's gapped (non-prelim): 130
length of query: 490
length of database: 14,973,337
effective HSP length: 103
effective length of query: 387
effective length of database: 8,527,803
effective search space: 3300259761
effective search space used: 3300259761
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)