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= psy8148
(390 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 243 bits (621), Expect = 9e-65, Method: Compositional matrix adjust.
Identities = 110/181 (60%), Positives = 136/181 (75%)
Query: 145 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 204
P+ FT EQ+ C+CE +QQ G+ ++L FLWSLP + + ESVL+A+AVVA+ R F
Sbjct: 375 PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 434
Query: 205 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDG 264
ELY ILESH F H +LQQLW++ HY E K+RGR LGAV KYR+R+KFPLP+TIWDG
Sbjct: 435 ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDG 494
Query: 265 EETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQ 324
EET YCFKE+SR L+E Y N YP+P EKR+L+E TGLT TQVSNWFKNRRQRDR +
Sbjct: 495 EETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 554
Query: 325 R 325
+
Sbjct: 555 K 555
Score = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 53/100 (53%), Positives = 69/100 (69%)
Query: 6 PNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFH 65
P+ FT EQ+ C+CE +QQ G+ ++L FLWSLP + + ESVL+A+AVVA+ R F
Sbjct: 375 PSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFR 434
Query: 66 ELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLG 105
ELY ILESH F H +LQQLW++ HY E K+RGR LG
Sbjct: 435 ELYKILESHQFSPHNHPKLQQLWLKAHYVEAEKLRGRPLG 474
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 29/42 (69%)
Query: 343 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
YP+ ++K+QL++ TGLT+ QV+NWF N R+R P NR
Sbjct: 25 YPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQSNR 66
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 288 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 322
YP+ ++K+QL++ TGLT+ QV+NWF N R+R P
Sbjct: 25 YPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP 59
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 288 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
YP DEK+Q++ T LTL QV+NWF N R+R
Sbjct: 34 YPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 343 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
YP DEK+Q++ T LTL QV+NWF N R+R
Sbjct: 34 YPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 26/33 (78%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ + K +L++ +G+T++QVSNWF N+R R
Sbjct: 27 NPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR 59
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 26/33 (78%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ + K +L++ +G+T++QVSNWF N+R R
Sbjct: 27 NPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR 59
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 288 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
YP+ +EK+ LSE T L+L Q+SNWF N R+R
Sbjct: 34 YPSEEEKQMLSEKTNLSLLQISNWFINARRR 64
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 343 YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
YP+ +EK+ LSE T L+L Q+SNWF N R+R
Sbjct: 34 YPSEEEKQMLSEKTNLSLLQISNWFINARRR 64
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 28 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 28 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
E+ + L+ CY N P+ K QL E+TGL+ + WF+N+R +D+ +RSI
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK---KRSI 63
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ CY N P+ K QL E+TGL+ + WF+N+R +D+
Sbjct: 17 TLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK 59
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 25/33 (75%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ + K +L+ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELARKCGITVSQVSNWFGNKRIR 58
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N YP+ + K +L+ G+T++QVSNWF N+R R
Sbjct: 26 NPYPSEEAKEELARKCGITVSQVSNWFGNKRIR 58
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
+ALK + +N++P E L+++TGL+ +V WF +RR
Sbjct: 21 SALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+ALK + +N++P E L+++TGL+ +V WF +RR
Sbjct: 21 SALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F + L++ +D N YP DE QLS + L + WF+N RQ+ R
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ +D N YP DE QLS + L + WF+N RQ+ R
Sbjct: 21 VLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>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 = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + +NRYP+ + +++ T LT +V WFKNRR
Sbjct: 18 LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + +NRYP+ + +++ T LT +V WFKNRR
Sbjct: 18 LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
LK Y KN++P+ E +L +ITGLT ++ WF + R R +
Sbjct: 21 LKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK 65
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
LK Y KN++P+ E +L +ITGLT ++ WF + R R +
Sbjct: 21 LKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK 65
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of
Human Homeobox Protein Tgif1, Northeast Structural
Genomics Consortium Target Hr4411b
Length = 89
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 326 SIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
S+Q R+ L E + N YP+ EK LS+ T L+ QV NWF N R+R
Sbjct: 16 SVQILRDWLYE-HRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62
Score = 34.7 bits (78), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 21/33 (63%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N YP+ EK LS+ T L+ QV NWF N R+R
Sbjct: 30 NAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L+ Y N++ D++R++S T L+ QV+ WF+NRR +++
Sbjct: 22 LEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ Y N++ D++R++S T L+ QV+ WF+NRR +++
Sbjct: 22 LEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + RY + E+ QL+ + LT TQV WF+NRR
Sbjct: 17 LERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
Score = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + RY + E+ QL+ + LT TQV WF+NRR
Sbjct: 17 LERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.7 bits (78), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L+ Y N++ D++R++S T L+ QV+ WF+NRR +++
Sbjct: 16 LEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
Score = 34.7 bits (78), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ Y N++ D++R++S T L+ QV+ WF+NRR +++
Sbjct: 16 LEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 28/42 (66%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L+ Y N++ D++R++S T L+ Q++ WF+NRR +++
Sbjct: 22 LEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
Score = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 28/42 (66%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ Y N++ D++R++S T L+ Q++ WF+NRR +++
Sbjct: 22 LEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>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 = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 22/38 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL QV WFKN R
Sbjct: 19 LKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMR 56
Score = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 22/38 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL QV WFKN R
Sbjct: 19 LKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMR 56
>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 = 34.7 bits (78), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WFKN+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
Score = 34.7 bits (78), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WFKN+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
>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 = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
F + ALK+ + K +Y + + ++LS I L+ QV WF+N+R
Sbjct: 10 FSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQR 55
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
ALK+ + K +Y + + ++LS I L+ QV WF+N+R
Sbjct: 17 ALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQR 55
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 25/40 (62%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
LK + ++++P+ E +L E+TGL +++ WF + R R
Sbjct: 19 LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 25/40 (62%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
LK + ++++P+ E +L E+TGL +++ WF + R R
Sbjct: 19 LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + +N YP+ + +++ T LT +V WFKNRR
Sbjct: 18 LEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + +N YP+ + +++ T LT +V WFKNRR
Sbjct: 18 LEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
AL+ + K +Y E+ +L+ GLT TQV WF+N+R +
Sbjct: 21 ALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
AL+ + K +Y E+ +L+ GLT TQV WF+N+R +
Sbjct: 21 ALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 6/52 (11%)
Query: 320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+TP+Q + LK + + ++P+P+E +L++ +GL T + +WF + R
Sbjct: 32 KTPEQLHM------LKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTR 77
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 256 PLPKTIWDGEETVYCFKERSR-NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN 314
P PK+ G C K + + LK + + ++P+P+E +L++ +GL T + +WF +
Sbjct: 19 PAPKS---GSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGD 75
Query: 315 RR 316
R
Sbjct: 76 TR 77
>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 = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 28/44 (63%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+ L+ +++ +YP+ + +L++ T LT ++ WF+NRR R R
Sbjct: 31 DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 28/44 (63%)
Query: 332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
+ L+ +++ +YP+ + +L++ T LT ++ WF+NRR R R
Sbjct: 31 DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%)
Query: 264 GEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
G + F E L++ ++K +Y + ++ L+E GL+ QV W++NRR +
Sbjct: 17 GRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 26/41 (63%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
L++ ++K +Y + ++ L+E GL+ QV W++NRR +
Sbjct: 31 GLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 29/42 (69%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ ++ +Y +P E+++L+++ L+ QV WF+NRR + R
Sbjct: 22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 29/42 (69%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ ++ +Y +P E+++L+++ L+ QV WF+NRR + R
Sbjct: 22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 51
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 51
>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 = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 55
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 55
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 53
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 53
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF N+R
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKR 51
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF N+R
Sbjct: 14 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKR 51
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 258 PKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 317
P+T + E+ +E +++NRY ++QLS GL Q+ WF+N+R
Sbjct: 6 PRTAFSSEQLARAKRE---------FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRA 56
Query: 318 RDR 320
+ R
Sbjct: 57 KIR 59
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 335 KECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
K +++NRY ++QLS GL Q+ WF+N+R + R
Sbjct: 19 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L++ + K YP+ + QL+ T LT +V WF+NRR
Sbjct: 24 LEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L++ + K YP+ + QL+ T LT +V WF+NRR
Sbjct: 24 LEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 32.0 bits (71), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 319
F + R L + +N+ P+ + + +S+ GL L+ VSN+F N R+R
Sbjct: 102 LVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRS 152
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
R L + +N+ P+ + + +S+ GL L+ VSN+F N R+R
Sbjct: 109 RRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRS 152
>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 = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF+N R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNER 53
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF+N R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNER 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.0 bits (71), Expect = 0.62, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 317 QRDRTPQQRSI--QRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
+++++P+ +S ++R L+E + + + N EK ++++ G+T QV WF N+R R
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60
Query: 375 R 375
+
Sbjct: 61 K 61
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 274 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
++R L+E + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 15 QARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 28/58 (48%)
Query: 263 DGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
G+ FK +K + N P+ + +QL++ TGLT + WF+N R + R
Sbjct: 6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
+K + N P+ + +QL++ TGLT + WF+N R + R
Sbjct: 21 TMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 32.0 bits (71), Expect = 0.67, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 317 QRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
+R+RT R+ + L+ + K RYP+ + +++ L ++V WFKNRR + R
Sbjct: 8 RRERTTFTRA---QLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64
Query: 377 PQQRAKN 383
QQ+ +N
Sbjct: 65 QQQQQQN 71
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F + L+ + K RYP+ + +++ L ++V WFKNRR + R
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WF+N R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNAR 53
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WF+N R
Sbjct: 16 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNAR 53
>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 = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 21 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 21 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F + AL+ + + +YP+ + QL+ L +V WFKNRR + R
Sbjct: 13 IFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
AL+ + + +YP+ + QL+ L +V WFKNRR + R
Sbjct: 21 ALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 274 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
++R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 329 RSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
++R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 275 SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 8 ARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 330 SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
+R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 8 ARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 283 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
+++NRY ++QLS GL Q+ WF+N+R
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 38
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 338 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+++NRY ++QLS GL Q+ WF+N+R
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 38
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 317 QRDRTPQQRSI--QRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
+++++P+ +S ++R L++ + + + N EK ++++ G+T QV WF N+R R
Sbjct: 1 KKEKSPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60
Query: 375 R 375
+
Sbjct: 61 K 61
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 275 SRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 16 ARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+RR++ RT + +I R AL++ + +N+ P +E +++ + + WF NRRQ+
Sbjct: 98 SRRRKKRTSIETNI---RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQK 154
Query: 374 DR 375
++
Sbjct: 155 EK 156
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L+ +++ YP+ + +L++ LT +V WF NRR R R
Sbjct: 17 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWR 58
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ +++ YP+ + +L++ LT +V WF NRR R R
Sbjct: 17 LERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWR 58
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+RR++ RT + +I R AL++ + +N+ P ++ ++E + + WF NRRQ+
Sbjct: 99 SRRRKKRTSIETNI---RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 155
Query: 374 DR 375
++
Sbjct: 156 EK 157
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
AL+ + + +Y + E+ + S LT TQV WF+NRR + +
Sbjct: 14 ALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
AL+ + + +Y + E+ + S LT TQV WF+NRR + +
Sbjct: 14 ALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 269 YCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
F + R L + +N+ P+ + + +S+ GL L+ VSN+F N R
Sbjct: 100 LVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 331 RNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
R L + +N+ P+ + + +S+ GL L+ VSN+F N R
Sbjct: 107 RRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%)
Query: 320 RTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
R P+ Q L+ + N YP D L++ L L ++ WF+NRR
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRR 53
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
F + L+ + N YP D L++ L L ++ WF+NRR
Sbjct: 7 AFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRR 53
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+RR++ RT + +I R AL++ + +N+ P +E +++ + + WF NRRQ+
Sbjct: 94 SRRRKKRTSIETNI---RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 150
Query: 374 DR 375
++
Sbjct: 151 EK 152
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
L+ + + RY + E+ L+ + LT TQV WF+N R + + Q
Sbjct: 27 LERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
L+ + + RY + E+ L+ + LT TQV WF+N R + + Q
Sbjct: 27 LERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
>pdb|2DA7|A Chain A, Solution Structure Of The Homeobox Domain Of Zinc Finger
Homeobox Protein 1b (Smad Interacting Protein 1)
Length = 71
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
+ LK Y N PN DE ++S GL V WF+ R+
Sbjct: 18 SVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRK 57
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+ LK Y N PN DE ++S GL V WF+ R+
Sbjct: 18 SVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRK 57
>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 = 2.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 323
L+ + + RY + E+ L+ + LT TQV WF+N R + + Q
Sbjct: 24 LERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
L+ + + RY + E+ L+ + LT TQV WF+N R + + Q
Sbjct: 24 LERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + +Y + E+ L+ + LT TQV WF+N R
Sbjct: 17 LERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHR 54
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + +Y + E+ L+ + LT TQV WF+N R
Sbjct: 17 LERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHR 54
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+RR++ RT + +I R AL++ + +N+ P +E +++ + + WF NRRQ+
Sbjct: 101 SRRRKKRTSIETNI---RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 157
Query: 374 DR 375
++
Sbjct: 158 EK 159
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
L+ + +Y + E+ L++ LT TQV WF+NRR + + Q S
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSS 66
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
L+ + +Y + E+ L++ LT TQV WF+NRR + + Q
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 254 KFPLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFK 313
K P+ K ++T F L + + + +Y + + ++LS I L+ QV WF+
Sbjct: 17 KVPVKK-----QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQ 71
Query: 314 NRRQRDR 320
N+R + +
Sbjct: 72 NQRMKSK 78
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L + + + +Y + + ++LS I L+ QV WF+N+R + +
Sbjct: 36 VLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
RR++ RT + +I R AL++ + +N+ P +E +++ + + WF NRRQ++
Sbjct: 6 RRRKKRTSIETNI---RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 62
Query: 375 R 375
+
Sbjct: 63 K 63
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
L++ + + RY LS L QV WFKNRR+R
Sbjct: 17 LEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 56
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
L++ + + RY LS L QV WFKNRR+R
Sbjct: 17 LEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 56
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 316 RQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
R++ RT + +I R AL++ + +N+ P +E +++ + + WF NRRQ+++
Sbjct: 104 RRKKRTSIETNI---RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>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 = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ--RDRTPQQRSIQR 329
L++ + K +Y E+ L+ +T QV WF+NRR R +T ++R +R
Sbjct: 32 LEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER 84
>pdb|2R5S|A Chain A, The Crystal Structure Of A Domain Of Protein Vp0806
(Unknown Function) From Vibrio Parahaemolyticus Rimd
2210633
pdb|2R5S|B Chain B, The Crystal Structure Of A Domain Of Protein Vp0806
(Unknown Function) From Vibrio Parahaemolyticus Rimd
2210633
Length = 176
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 113 PVLYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCE-AMQ--QSGDFDK 169
P+ Y+ N++ LE+ Q+A E +K+L ++ P+ + CE A+Q Q G ++
Sbjct: 67 PLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEE 126
Query: 170 LAMFLWSL 177
LW++
Sbjct: 127 ALELLWNI 134
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
N Y D + +++ + LT QV WF+NRR +
Sbjct: 23 NMYLTRDRRYEVARVLNLTERQVKIWFQNRRMK 55
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
N Y D + +++ + LT QV WF+NRR +
Sbjct: 23 NMYLTRDRRYEVARVLNLTERQVKIWFQNRRMK 55
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 41/187 (21%), Positives = 74/187 (39%), Gaps = 24/187 (12%)
Query: 70 ILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLE 129
+L+ H + +HA+ + M H K+ K+ G + + D L +A DF+ +++
Sbjct: 459 LLDKHGYTGIFHAKARAKTM--HSKDSKKVDGCCIFFKRDQFK--LITKDAMDFSGAWMK 514
Query: 130 IQ--QKAQEYLN--MKKLNPNMSFTPEQIDCLCEAMQQSGD--FDKLAMFLWSLPPQEAI 183
+ Q+ ++YLN M K N + + I SGD + W +
Sbjct: 515 HKKFQRTEDYLNRAMNKDNVALFLKLQHI--------PSGDTIWAVTTHLHWDPKFNDVK 566
Query: 184 RGQESVLRARAVVAYKRHAFHEL------YAILESHNFDSKYHAELQQLWMRGHYKEHAK 237
Q VL K H + +L +F+S ++ + +L G + H +
Sbjct: 567 TFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQE 626
Query: 238 IRGRDLG 244
GRD G
Sbjct: 627 GNGRDFG 633
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
0.319 0.133 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,082,029
Number of Sequences: 62578
Number of extensions: 496737
Number of successful extensions: 1180
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 78
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1020
Number of HSP's gapped (non-prelim): 176
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
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: 52 (24.6 bits)