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= psy16496
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HO5|H Chain H, Crystal Structure Of Hedgehog-interacting Protein (hhip)
And Sonic Hedgehog (shh) Complex
pdb|3MXW|A Chain A, Crystal Structure Sonic Hedgehog Bound To The 5e1 Fab
Fragment
Length = 169
Score = 166 bits (421), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 76/99 (76%), Positives = 86/99 (86%), Gaps = 1/99 (1%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 72 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 131
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETTHVNGKGAG 114
+LAR+AVEAGFDWVYYES+ HIHCSVK E + V K G
Sbjct: 132 MLARLAVEAGFDWVYYESKAHIHCSVKAENS-VAAKSGG 169
>pdb|3M1N|A Chain A, Crystal Structure Of Human Sonic Hedgehog N-Terminal
Domain
pdb|3M1N|B Chain B, Crystal Structure Of Human Sonic Hedgehog N-Terminal
Domain
Length = 175
Score = 166 bits (421), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 76/99 (76%), Positives = 86/99 (86%), Gaps = 1/99 (1%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 78 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 137
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETTHVNGKGAG 114
+LAR+AVEAGFDWVYYES+ HIHCSVK E + V K G
Sbjct: 138 MLARLAVEAGFDWVYYESKAHIHCSVKAENS-VAAKSGG 175
>pdb|3N1R|A Chain A, Crystal Structure Of Shhn
Length = 160
Score = 166 bits (420), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 73/91 (80%), Positives = 83/91 (91%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 66 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 125
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
+LAR+AVEAGFDWVYYES+ HIHCSVK E +
Sbjct: 126 MLARLAVEAGFDWVYYESKAHIHCSVKAENS 156
>pdb|1VHH|A Chain A, A Potential Catalytic Site Within The Amino-Terminal
Signalling Domain Of Sonic Hedgehog
Length = 162
Score = 166 bits (420), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 73/91 (80%), Positives = 83/91 (91%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 68 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 127
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
+LAR+AVEAGFDWVYYES+ HIHCSVK E +
Sbjct: 128 MLARLAVEAGFDWVYYESKAHIHCSVKAENS 158
>pdb|2WG4|A Chain A, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog Without
Calcium
Length = 155
Score = 166 bits (420), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 73/91 (80%), Positives = 83/91 (91%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 62 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 121
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
+LAR+AVEAGFDWVYYES+ HIHCSVK E +
Sbjct: 122 MLARLAVEAGFDWVYYESKAHIHCSVKAENS 152
>pdb|2WFX|A Chain A, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog In The
Presence Of Calcium
Length = 152
Score = 166 bits (419), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 73/91 (80%), Positives = 83/91 (91%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 62 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 121
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
+LAR+AVEAGFDWVYYES+ HIHCSVK E +
Sbjct: 122 MLARLAVEAGFDWVYYESKAHIHCSVKAENS 152
>pdb|3D1M|A Chain A, Crystal Structure Of Sonic Hedgehog Bound To The Third
Fniii Domain Of Cdo
pdb|3D1M|B Chain B, Crystal Structure Of Sonic Hedgehog Bound To The Third
Fniii Domain Of Cdo
Length = 168
Score = 165 bits (418), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 73/89 (82%), Positives = 82/89 (92%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 80 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 139
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
+LAR+AVEAGFDWVYYES+ HIHCSVK E
Sbjct: 140 MLARLAVEAGFDWVYYESKAHIHCSVKAE 168
>pdb|3K7H|B Chain B, Crystal Structure Of The E95k Mutant Of The Indian
Hedgehog N-Terminal Signalling Domain
Length = 187
Score = 164 bits (415), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 71/89 (79%), Positives = 84/89 (94%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K++LN+LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD +KYG
Sbjct: 90 QRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYG 149
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYES+ H+HCSVK+E
Sbjct: 150 LLARLAVEAGFDWVYYESKAHVHCSVKSE 178
>pdb|3K7J|B Chain B, Crystal Structure Of The D100e Mutant Of The Indian
Hedgehog N- Terminal Signalling Domain
Length = 187
Score = 164 bits (415), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 71/89 (79%), Positives = 84/89 (94%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K++LN+LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD +KYG
Sbjct: 90 QRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYG 149
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYES+ H+HCSVK+E
Sbjct: 150 LLARLAVEAGFDWVYYESKAHVHCSVKSE 178
>pdb|3K7G|B Chain B, Crystal Structure Of The Indian Hedgehog N-Terminal
Signalling Domain
Length = 187
Score = 164 bits (415), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 71/89 (79%), Positives = 84/89 (94%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K++LN+LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD +KYG
Sbjct: 90 QRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYG 149
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYES+ H+HCSVK+E
Sbjct: 150 LLARLAVEAGFDWVYYESKAHVHCSVKSE 178
>pdb|3N1F|A Chain A, Crystal Structure Of Ihhn Bound To Cdofn3
pdb|3N1F|B Chain B, Crystal Structure Of Ihhn Bound To Cdofn3
pdb|3N1M|B Chain B, Crystal Structure Of Ihhn Bound To Bocfn3
pdb|3N1O|A Chain A, Crystal Structure Of Ihhn
pdb|3N1O|B Chain B, Crystal Structure Of Ihhn
pdb|3N1O|C Chain C, Crystal Structure Of Ihhn
pdb|3N1P|B Chain B, Crystal Structure Of Ihhn Bound To Bocfn3
Length = 169
Score = 164 bits (414), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 71/89 (79%), Positives = 84/89 (94%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K++LN+LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD +KYG
Sbjct: 81 QRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYG 140
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYES+ H+HCSVK+E
Sbjct: 141 LLARLAVEAGFDWVYYESKAHVHCSVKSE 169
>pdb|3K7I|B Chain B, Crystal Structure Of The E131k Mutant Of The Indian
Hedgehog N- Terminal Signalling Domain
Length = 187
Score = 162 bits (411), Expect = 1e-40, Method: Compositional matrix adjust.
Identities = 70/89 (78%), Positives = 84/89 (94%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K++LN+LAISVMN+WPGV+LRV +GWDE+GHH+ +SLHYEGRAVDITTSDRD +KYG
Sbjct: 90 QRCKDRLNSLAISVMNQWPGVKLRVTKGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYG 149
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYES+ H+HCSVK+E
Sbjct: 150 LLARLAVEAGFDWVYYESKAHVHCSVKSE 178
>pdb|2WFQ|A Chain A, Crystal Structure Of The N-terminal Signalling Domain Of
Human Dhh Without Calcium
pdb|2WFR|A Chain A, Crystal Structure Of The N-Terminal Signalling Domain Of
Human Dhh With Calcium
Length = 165
Score = 161 bits (407), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 71/91 (78%), Positives = 82/91 (90%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
+R KE++N LAI+VMN WPGVRLRV EGWDE+GHHA DSLHYEGRA+DITTSDRD +KYG
Sbjct: 63 ERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYG 122
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
LLAR+AVEAGFDWVYYESRNH+H SVK + +
Sbjct: 123 LLARLAVEAGFDWVYYESRNHVHVSVKADNS 153
>pdb|2WG3|A Chain A, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Desert Hedgehog Without
Calcium
pdb|2WG3|B Chain B, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Desert Hedgehog Without
Calcium
Length = 164
Score = 161 bits (407), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 71/91 (78%), Positives = 82/91 (90%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
+R KE++N LAI+VMN WPGVRLRV EGWDE+GHHA DSLHYEGRA+DITTSDRD +KYG
Sbjct: 63 ERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYG 122
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTETT 106
LLAR+AVEAGFDWVYYESRNH+H SVK + +
Sbjct: 123 LLARLAVEAGFDWVYYESRNHVHVSVKADNS 153
>pdb|3N1G|B Chain B, Crystal Structure Of Dhhn Bound To Bocfn3
pdb|3N1G|A Chain A, Crystal Structure Of Dhhn Bound To Bocfn3
pdb|3N1Q|B Chain B, Crystal Structure Of Dhhn Bound To Cdofn3
pdb|3N1Q|A Chain A, Crystal Structure Of Dhhn Bound To Cdofn3
pdb|3N1Q|E Chain E, Crystal Structure Of Dhhn Bound To Cdofn3
Length = 170
Score = 160 bits (405), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 71/89 (79%), Positives = 81/89 (91%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
+R KE++N LAI+VMN WPGVRLRV EGWDE+GHHA DSLHYEGRA+DITTSDRD +KYG
Sbjct: 82 ERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYG 141
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
LLAR+AVEAGFDWVYYESRNH+H SVK +
Sbjct: 142 LLARLAVEAGFDWVYYESRNHVHVSVKAD 170
>pdb|2IBG|E Chain E, Crystal Structure Of Hedgehog Bound To The Fniii Domains
Of Ihog
pdb|2IBG|F Chain F, Crystal Structure Of Hedgehog Bound To The Fniii Domains
Of Ihog
pdb|2IBG|G Chain G, Crystal Structure Of Hedgehog Bound To The Fniii Domains
Of Ihog
pdb|2IBG|H Chain H, Crystal Structure Of Hedgehog Bound To The Fniii Domains
Of Ihog
Length = 150
Score = 143 bits (361), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 65/89 (73%), Positives = 74/89 (83%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
+R KEKLN LA SVMNEWPG+RL V E WDE+ HH +SLHYEGRAV I TSDRD SKYG
Sbjct: 62 KRCKEKLNVLAYSVMNEWPGIRLLVTESWDEDYHHGQESLHYEGRAVTIATSDRDQSKYG 121
Query: 76 LLARMAVEAGFDWVYYESRNHIHCSVKTE 104
+LAR+AVEAGFDWV Y SR HI+CSVK++
Sbjct: 122 MLARLAVEAGFDWVSYVSRRHIYCSVKSD 150
>pdb|1AT0|A Chain A, 17-Kda Fragment Of Hedgehog C-Terminal Autoprocessing
Domain
Length = 145
Score = 72.0 bits (175), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 36/107 (33%), Positives = 64/107 (59%), Gaps = 6/107 (5%)
Query: 115 CFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQIT 174
CFT +ST L++ + +L+IGD+VL+ T G+ YSEV+LF R+ NFVQ+
Sbjct: 1 CFTPESTALLESGVRKPLGELSIGDRVLS-XTANGQAVYSEVILFXDRNLEQXQNFVQLH 59
Query: 175 TESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVH 221
T+ G+++ +TP+HL+ W + K + + +A+R+ + ++V
Sbjct: 60 TDGGAVLTVTPAHLVSVWQPESQK-----LTFVFADRIEEKNQVLVR 101
>pdb|4A0B|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
pdb|4A0B|C Chain C, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
Length = 1159
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 453 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 510
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 511 EPQAKNI 517
>pdb|4A08|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 13 Bp Cpd-Duplex (
Purine At D-1 Position) At 3.0 A Resolution (Cpd 1)
pdb|4A09|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 15 Bp Cpd-Duplex
(Purine At D-1 Position) At 3.1 A Resolution (Cpd 2)
Length = 1159
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 453 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 510
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 511 EPQAKNI 517
>pdb|4A0L|A Chain A, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|C Chain C, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1144
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 438 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 495
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 496 EPQAKNI 502
>pdb|4A0A|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.6 A Resolution (Cpd 3)
Length = 1159
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 453 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 510
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 511 EPQAKNI 517
>pdb|2B5L|A Chain A, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5L|B Chain B, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5M|A Chain A, Crystal Structure Of Ddb1
pdb|2HYE|A Chain A, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 1140
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 434 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 491
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 492 EPQAKNI 498
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 434 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 491
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 492 EPQAKNI 498
>pdb|4E54|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
pdb|4E5Z|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
Length = 1150
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 444 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 501
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 502 EPQAKNI 508
>pdb|4A11|A Chain A, Structure Of The Hsddb1-Hscsa Complex
pdb|4A0K|C Chain C, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1159
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 453 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 510
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 511 EPQAKNI 517
>pdb|3EI1|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 14 Bp 6-4
Photoproduct Containing Dna-Duplex
pdb|3EI2|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Abasic Site
Containing Dna-Duplex
pdb|3EI3|A Chain A, Structure Of The Hsddb1-Drddb2 Complex
Length = 1158
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 452 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 509
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 510 EPQAKNI 516
>pdb|3I7H|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Hbx
pdb|3I7K|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Whx
pdb|3I7L|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Ddb2
pdb|3I7N|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdtc1
pdb|3I7O|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Iqwd1
pdb|3I7P|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr40a
pdb|3I89|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr22
pdb|3I8C|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr21a
pdb|3I8E|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
pdb|3I8E|B Chain B, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
Length = 1143
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 437 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 494
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 495 EPQAKNI 501
>pdb|3EI4|A Chain A, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|C Chain C, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|E Chain E, Structure Of The Hsddb1-Hsddb2 Complex
Length = 1158
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 452 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 509
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 510 EPQAKNI 516
>pdb|4E2U|A Chain A, Crystal Structures Of Radamin Intein From Pyrococcus
Horikoshii
Length = 168
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 32/139 (23%), Positives = 62/139 (44%), Gaps = 25/139 (17%)
Query: 89 VYYESRN--HIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNT 146
VYYE+ H+ + + + + G F V LDN V TL+
Sbjct: 12 VYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDN------------VFVYTLDI 59
Query: 147 ITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEY 206
+GE++ + +++R+ V ++I SG +K+TPSH +L + + +++
Sbjct: 60 ASGEIKKTRAS-YIYREK--VEKLIEIKLSSGYSLKVTPSHPVLLFR--------DGLQW 108
Query: 207 TYAERVRVNDSIIVHKNGK 225
A V+ D ++ +NG+
Sbjct: 109 VPAAEVKPGDVVVGVRNGE 127
>pdb|2B5N|A Chain A, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|B Chain B, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|C Chain C, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|D Chain D, Crystal Structure Of The Ddb1 Bpb Domain
Length = 323
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 140 KVLTLNTITGEMEYSEVLLFLHRDP-----NLVHN-FVQITTESGSLIKMTPSHLILRWH 193
+VL LN E+E +E++ F+ N+ H +QIT+ S L+ P L+ W
Sbjct: 48 RVLMLNG--EEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWK 105
Query: 194 RPNAKSI 200
P AK+I
Sbjct: 106 EPQAKNI 112
>pdb|2LQM|A Chain A, Solution Structures Of Rada Intein From Pyrococcus
Horikoshii
pdb|4E2T|A Chain A, Crystal Structures Of Rada Intein From Pyrococcus
Horikoshii
pdb|4E2T|B Chain B, Crystal Structures Of Rada Intein From Pyrococcus
Horikoshii
Length = 174
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 27/104 (25%), Positives = 47/104 (45%), Gaps = 17/104 (16%)
Query: 89 VYYESRN--HIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNT 146
VYYE+ H+ + + + + G F V LDN V TL+
Sbjct: 8 VYYENDTVPHMESIEEMYSKYASMNGELPFDNGYAVPLDNVF------------VYTLDI 55
Query: 147 ITGEMEYSEVLLFLHRDPNLVHNFVQITTESGSLIKMTPSHLIL 190
+GE++ + +++R+ V ++I SG +K+TPSH +L
Sbjct: 56 ASGEIKKTRAS-YIYREK--VEKLIEIKLSSGYSLKVTPSHPVL 96
>pdb|2OV9|A Chain A, Crystal Structure Of Protein Rha08564, Thioesterase
Superfamily Protein
pdb|2OV9|B Chain B, Crystal Structure Of Protein Rha08564, Thioesterase
Superfamily Protein
pdb|2OV9|C Chain C, Crystal Structure Of Protein Rha08564, Thioesterase
Superfamily Protein
pdb|2OV9|D Chain D, Crystal Structure Of Protein Rha08564, Thioesterase
Superfamily Protein
Length = 216
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 15 FQRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEG 48
+R+ E+LN++A + P V R+I+ W+ EG
Sbjct: 51 LERVAEELNSIAGHLEEHAPAVAERLIDXWNGEG 84
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 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,013,700
Number of Sequences: 62578
Number of extensions: 279767
Number of successful extensions: 767
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 736
Number of HSP's gapped (non-prelim): 35
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
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: 50 (23.9 bits)