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= 003173
(842 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 742
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 50/212 (23%), Positives = 86/212 (40%), Gaps = 17/212 (8%)
Query: 542 RKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQR 601
R +D + ++ I KD Y+ LA +LL +D+E L LK G + +
Sbjct: 414 RTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSK 473
Query: 602 CEIMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWP---PMQD 658
E M D+ SK + K ++ Q I++ +WP PM
Sbjct: 474 LEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT---------VNILTMGYWPTYTPM-- 522
Query: 659 EALIVPGHIDQLLADYAKRFNEIK-TPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAA 717
E + P I L + K F K + RKL W+ LG L+ +F + +F V+
Sbjct: 523 EVHLTPEMIK--LQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTL 580
Query: 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRIN 749
+++ F + ++ + + A G+ L R +
Sbjct: 581 VLLMFNEGDGFSFEEIKMATGIEDSELRRTLQ 612
>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 759
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 50/212 (23%), Positives = 86/212 (40%), Gaps = 17/212 (8%)
Query: 542 RKVDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQR 601
R +D + ++ I KD Y+ LA +LL +D+E L LK G + +
Sbjct: 431 RTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSK 490
Query: 602 CEIMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWP---PMQD 658
E M D+ SK + K ++ Q I++ +WP PM
Sbjct: 491 LEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT---------VNILTMGYWPTYTPM-- 539
Query: 659 EALIVPGHIDQLLADYAKRFNEIK-TPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAA 717
E + P I L + K F K + RKL W+ LG L+ +F + +F V+
Sbjct: 540 EVHLTPEMIK--LQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTL 597
Query: 718 IIMQFQDQTSWTSKNLAAAVGVPVDVLSRRIN 749
+++ F + ++ + + A G+ L R +
Sbjct: 598 VLLMFNEGDGFSFEEIKMATGIEDSELRRTLQ 629
>pdb|1U6G|A Chain A, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
Length = 776
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/209 (18%), Positives = 79/209 (37%), Gaps = 10/209 (4%)
Query: 549 MIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLND 608
++ I KD Y MLA +L++++ D+E + LK G + + M D
Sbjct: 451 VVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQD 510
Query: 609 LIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIVPGHID 668
+ SK N K + ++SS WP Q +P ++
Sbjct: 511 IGVSKDLNEQFKKHL----------TNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELE 560
Query: 669 QLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSW 728
+ + + + RKL W L +L + AI++Q+ + ++
Sbjct: 561 RSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAY 620
Query: 729 TSKNLAAAVGVPVDVLSRRINFWISKGII 757
T + L + + +D+L++ + + ++
Sbjct: 621 TVQQLTDSTQIKMDILAQVLQILLKSKLL 649
>pdb|1LDJ|A Chain A, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 760
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/209 (18%), Positives = 79/209 (37%), Gaps = 10/209 (4%)
Query: 549 MIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLND 608
++ I KD Y MLA +L++++ D+E + LK G + + M D
Sbjct: 435 VVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQD 494
Query: 609 LIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIVPGHID 668
+ SK N K + ++SS WP Q +P ++
Sbjct: 495 IGVSKDLNEQFKKHL----------TNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELE 544
Query: 669 QLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSW 728
+ + + + RKL W L +L + AI++Q+ + ++
Sbjct: 545 RSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAY 604
Query: 729 TSKNLAAAVGVPVDVLSRRINFWISKGII 757
T + L + + +D+L++ + + ++
Sbjct: 605 TVQQLTDSTQIKMDILAQVLQILLKSKLL 633
>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|H Chain H, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 726
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 42/203 (20%), Positives = 79/203 (38%), Gaps = 9/203 (4%)
Query: 544 VDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCE 603
+D + +I I KD Y+ LA +LL +D+E L LK G + + E
Sbjct: 400 LDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLE 459
Query: 604 IMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIV 663
M D+ SK K ++ Q I++ +WP + +
Sbjct: 460 GMFKDMELSKDIMIQFKQYMQNQNVPGNIELT---------VNILTMGYWPTYVPMEVHL 510
Query: 664 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQ 723
P + +L + + + RKL W+ LG L+ +F + + V+ +++ F
Sbjct: 511 PPEMVKLQEIFKTFYLGKHSGRKLQWQSTLGHCVLKAEFKEGKKELQVSLFQTLVLLMFN 570
Query: 724 DQTSWTSKNLAAAVGVPVDVLSR 746
+ ++ + + A G+ L R
Sbjct: 571 EGEEFSLEEIKQATGIEDGELRR 593
>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|E Chain E, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 741
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 42/205 (20%), Positives = 80/205 (39%), Gaps = 9/205 (4%)
Query: 544 VDILGMIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCE 603
+D + +I I KD Y+ LA +LL +D+E L LK G + + E
Sbjct: 415 LDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLE 474
Query: 604 IMLNDLIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIV 663
M D+ SK K ++ Q I++ +WP + +
Sbjct: 475 GMFKDMELSKDIMIQFKQYMQNQNVPGNIELT---------VNILTMGYWPTYVPMEVHL 525
Query: 664 PGHIDQLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQ 723
P + +L + + + RKL W+ LG L+ +F + + V+ +++ F
Sbjct: 526 PPEMVKLQEIFKTFYLGKHSGRKLQWQSTLGHCVLKAEFKEGKKELQVSLFQTLVLLMFN 585
Query: 724 DQTSWTSKNLAAAVGVPVDVLSRRI 748
+ ++ + + A G+ L R +
Sbjct: 586 EGEEFSLEEIKQATGIEDGELRRTL 610
>pdb|4F52|A Chain A, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|C Chain C, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 282
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 38/204 (18%), Positives = 77/204 (37%), Gaps = 10/204 (4%)
Query: 554 IGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSK 613
I KD Y MLA +L++++ D+E + LK G + + M D+ SK
Sbjct: 48 IEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSK 107
Query: 614 RTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIVPGHIDQLLAD 673
N K + ++SS WP Q +P +++
Sbjct: 108 DLNEQFKKHL----------TNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQR 157
Query: 674 YAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNL 733
+ + + RKL W L +L + AI++Q+ + ++T + L
Sbjct: 158 FTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQL 217
Query: 734 AAAVGVPVDVLSRRINFWISKGII 757
+ + +D+L++ + + ++
Sbjct: 218 TDSTQIKMDILAQVLQILLKSKLL 241
>pdb|1LDK|B Chain B, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 366
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 38/209 (18%), Positives = 79/209 (37%), Gaps = 10/209 (4%)
Query: 549 MIVGIIGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLND 608
++ I KD Y MLA +L++++ D+E + LK G + + M D
Sbjct: 41 VVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQD 100
Query: 609 LIDSKRTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIVPGHID 668
+ SK N K + ++SS WP Q +P ++
Sbjct: 101 IGVSKDLNEQFKKHL----------TNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELE 150
Query: 669 QLLADYAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSW 728
+ + + + RKL W L +L + AI++Q+ + ++
Sbjct: 151 RSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAY 210
Query: 729 TSKNLAAAVGVPVDVLSRRINFWISKGII 757
T + L + + +D+L++ + + ++
Sbjct: 211 TVQQLTDSTQIKMDILAQVLQILLKSKLL 239
>pdb|3RTR|A Chain A, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|C Chain C, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|E Chain E, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|G Chain G, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
Length = 368
Score = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 38/204 (18%), Positives = 77/204 (37%), Gaps = 10/204 (4%)
Query: 554 IGSKDQLVNEYRVMLADKLLNKSDYEIDSEIRTLELLKIHFGESSMQRCEIMLNDLIDSK 613
I KD Y MLA +L++++ D+E + LK G + + M D+ SK
Sbjct: 48 IEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSK 107
Query: 614 RTNANIKATIEKQXXXXXXXXXXXXXXXXXDATIISSNFWPPMQDEALIVPGHIDQLLAD 673
N K + ++SS WP Q +P +++
Sbjct: 108 DLNEQFKKHL----------TNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQR 157
Query: 674 YAKRFNEIKTPRKLLWKKNLGTVKLELQFDDRAMQFTVAPIHAAIIMQFQDQTSWTSKNL 733
+ + + RKL W L +L + AI++Q+ + ++T + L
Sbjct: 158 FTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQL 217
Query: 734 AAAVGVPVDVLSRRINFWISKGII 757
+ + +D+L++ + + ++
Sbjct: 218 TDSTQIKMDILAQVLQILLKSKLL 241
>pdb|3SF5|B Chain B, Crystal Structure Of Helicobacter Pylori Urease Accessory
Protein UrefH COMPLEX
pdb|3SF5|D Chain D, Crystal Structure Of Helicobacter Pylori Urease Accessory
Protein UrefH COMPLEX
Length = 265
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 47/101 (46%), Gaps = 7/101 (6%)
Query: 82 RTFVSKFWRHFDVYSKVAVLEKNKPLIYDDEVHEVLCKALEEICMEIQYQEKCLFMLVHA 141
R + KF R +++K+++L+ KP+ YD+ + + L +CM Y +LV+
Sbjct: 149 RNELFKFNR---LHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNC 205
Query: 142 ---IESPRDCSLEGKPILDSEVHLFAKYQLMVSSVLMASLP 179
+ R+C E + + D V A L V ++ S P
Sbjct: 206 PIELSGVRECIEESEGV-DGAVSETASSHLCVKALAKGSEP 245
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,320,738
Number of Sequences: 62578
Number of extensions: 1030256
Number of successful extensions: 2331
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2312
Number of HSP's gapped (non-prelim): 13
length of query: 842
length of database: 14,973,337
effective HSP length: 107
effective length of query: 735
effective length of database: 8,277,491
effective search space: 6083955885
effective search space used: 6083955885
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)