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= 000237
(1806 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 176 bits (446), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 104/325 (32%), Positives = 173/325 (53%), Gaps = 44/325 (13%)
Query: 1442 LKVTLRRYQQEGINWLAFLKRFKLHGILCDDMGLGKTLQASAIVASDIAERRASNSIEEI 1501
+K LR YQ +G +W+ F+ + L DDMGLGKTLQ A+ + E E+
Sbjct: 34 IKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKE-------NEL 86
Query: 1502 HPSLIICPSTLVGHWAFEIEKFIDVSLMSTLQYVGSAQDRIALREQFDKHNVIITSYDVV 1561
PSL+ICP +++ +W E+ KF L++ +DR ++ + +++I+T+Y V+
Sbjct: 87 TPSLVICPLSVLKNWEEELSKF-----APHLRFAVFHEDRSKIK--LEDYDIILTTYAVL 139
Query: 1562 RKDADYLGQLLWNYCILDEGHIIKNSKSKITVAVKQLKAAHRLILSGTPIQNNITDLWSL 1621
+D L ++ W Y ++DE IKN ++KI AVK+LK+ +R+ L+GTPI+N + DLWS+
Sbjct: 140 LRDTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSI 198
Query: 1622 FDFLMPGFLGTERQFQATYGKPLVAARDSKCSAKDAEAGVLAMEALHKQVMPFLLRRTKD 1681
FL PG LG+ +F++ + P+ + +A E L + PF+LRRTK
Sbjct: 199 MTFLNPGLLGSYSEFKSKFATPIKKGDN------------MAKEELKAIISPFILRRTKY 246
Query: 1682 E--VLSDLPEKIIQDRYCDLSAVQLKLYEKFSGSQAKQEISSMVKVDESADKGEGNNVSA 1739
+ +++DLP+KI + YC+L+ Q +Y K E+ ++ +S
Sbjct: 247 DKAIINDLPDKIETNVYCNLTPEQAAMY--------KAEVENLFNNIDSV-------TGI 291
Query: 1740 KASTHVFQALQYLLKLCSHPLLVLG 1764
K + L L ++ HP L+ G
Sbjct: 292 KRKGMILSTLLKLKQIVDHPALLKG 316
>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX With
Dsdna
pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX With
Dsdna
Length = 500
Score = 168 bits (425), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 103/325 (31%), Positives = 168/325 (51%), Gaps = 44/325 (13%)
Query: 1442 LKVTLRRYQQEGINWLAFLKRFKLHGILCDDMGLGKTLQASAIVASDIAERRASNSIEEI 1501
+K LR YQ +G +W F + L DD GLGKTLQ A+ + E E+
Sbjct: 34 IKANLRPYQIKGFSWXRFXNKLGFGICLADDXGLGKTLQTIAVFSDAKKEN-------EL 86
Query: 1502 HPSLIICPSTLVGHWAFEIEKFIDVSLMSTLQYVGSAQDRIALREQFDKHNVIITSYDVV 1561
PSL+ICP +++ +W E+ KF L++ +DR ++ + +++I+T+Y V+
Sbjct: 87 TPSLVICPLSVLKNWEEELSKF-----APHLRFAVFHEDRSKIK--LEDYDIILTTYAVL 139
Query: 1562 RKDADYLGQLLWNYCILDEGHIIKNSKSKITVAVKQLKAAHRLILSGTPIQNNITDLWSL 1621
+D L ++ W Y ++DE IKN ++KI AVK+LK+ +R+ L+GTPI+N + DLWS+
Sbjct: 140 LRDTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSI 198
Query: 1622 FDFLMPGFLGTERQFQATYGKPLVAARDSKCSAKDAEAGVLAMEALHKQVMPFLLRRTKD 1681
FL PG LG+ +F++ + P+ + A E L + PF+LRRTK
Sbjct: 199 XTFLNPGLLGSYSEFKSKFATPIKKGDNX------------AKEELKAIISPFILRRTKY 246
Query: 1682 E--VLSDLPEKIIQDRYCDLSAVQLKLYEKFSGSQAKQEISSMVKVDESADKGEGNNVSA 1739
+ +++DLP+KI + YC+L+ Q Y K E+ ++ +S
Sbjct: 247 DKAIINDLPDKIETNVYCNLTPEQAAXY--------KAEVENLFNNIDSV-------TGI 291
Query: 1740 KASTHVFQALQYLLKLCSHPLLVLG 1764
K + L L ++ HP L+ G
Sbjct: 292 KRKGXILSTLLKLKQIVDHPALLKG 316
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of The
Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 145 bits (366), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 88/275 (32%), Positives = 148/275 (53%), Gaps = 35/275 (12%)
Query: 1446 LRRYQQEGINWLAFLKRFKLHGILCDDMGLGKTLQASAIVASDIAERRASNSIEEIHPSL 1505
LR +Q GINW+AFL +GIL D+MGLGKT+Q A ++ I RR + P +
Sbjct: 237 LRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNG------PHI 290
Query: 1506 IICPSTLVGHWAFEIEKFIDVSLMSTLQYVGSAQDRIALRE------------QFDKHNV 1553
I+ P + + W EK+ ++ + Y+G+ + R +RE + K NV
Sbjct: 291 IVVPLSTMPAWLDTFEKW--APDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNV 348
Query: 1554 IITSYDVVRKDADYLGQLLWNYCILDEGHIIKNSKSKITVAVKQLKAAHRLILSGTPIQN 1613
++T+Y+ + KD LG + W + +DE H +KN++S + ++ K A+R++++GTP+QN
Sbjct: 349 LLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQN 408
Query: 1614 NITDLWSLFDFLMPGFLGTERQFQATYGKPLVAARDSKCSAKDAEAGVLAMEALHKQVMP 1673
NI +L +L +FLMPG +++ D + ++ E + LH+++ P
Sbjct: 409 NIKELAALVNFLMPGRFTIDQEI------------DFENQDEEQEEYI---HDLHRRIQP 453
Query: 1674 FLLRRTKDEVLSDLPEKIIQDRYCDLSAVQLKLYE 1708
F+LRR K +V LP K + +LS VQ + Y+
Sbjct: 454 FILRRLKKDVEKSLPSKTERILRVELSDVQTEYYK 488
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 130 bits (327), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 103/333 (30%), Positives = 169/333 (50%), Gaps = 30/333 (9%)
Query: 1442 LKVTLRRYQQEGINWL---AFLKRFK--LHGILCDDMGLGKTLQASAIVASDIAERRASN 1496
L LR +Q+EG+ +L +R + I+ D+MGLGKTLQ ++ + + +++ +
Sbjct: 52 LSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLL--KQSPD 109
Query: 1497 SIEEIHPSLIICPSTLVGHWAFEIEKFIDVSLMSTLQYVGSAQDRIALREQFDKHN---- 1552
EI +++ PS+LV +W E+ K++ + GS + + F
Sbjct: 110 CKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRI 169
Query: 1553 ---VIITSYDVVRKDADYLGQLLWNYCILDEGHIIKNSKSKITVAVKQLKAAHRLILSGT 1609
++I SY+ R A+ L + I DEGH +KNS ++ +A+ + A R+++SGT
Sbjct: 170 PTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGT 229
Query: 1610 PIQNNITDLWSLFDFLMPGFLGTERQFQATYGKPLVAARDSKCSAKDAEAGVLAMEALHK 1669
PIQN++ + +SL F+ G LGT ++F+ + P++ RD+ S KD AG ++ L
Sbjct: 230 PIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQELIS 289
Query: 1670 QVMPFLLRRTKDEVLSDLPEKIIQDRYCDLSAVQLKLYEKFSGSQAKQEISSMVKVDESA 1729
V L+RRT D + LP KI Q C+L+ +Q +LY+ F QAK ES
Sbjct: 290 IVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFL-KQAKPV--------ESL 340
Query: 1730 DKGEGNNVSAKASTHVFQALQYLLKLCSHPLLV 1762
G K S ++ L KLC+HP L+
Sbjct: 341 QTG-------KISVSSLSSITSLKKLCNHPALI 366
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT Recycles
Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT Recycles
Rna Polymerase During Transcription
Length = 968
Score = 55.8 bits (133), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 58/211 (27%), Positives = 93/211 (44%), Gaps = 30/211 (14%)
Query: 1468 ILCDDMGLGKTLQASAIVASDIAERRASNSIEEIHPSLIICPSTLVGHWAFE-IEKF-ID 1525
+L D++GLGKT++A I+ + S + E + LII P TL W E + +F +
Sbjct: 174 LLADEVGLGKTIEAGXILHQQL----LSGAAERV---LIIVPETLQHQWLVEXLRRFNLR 226
Query: 1526 VSLMSTLQYVGSAQDRIALREQFDKHNVIITSYDVVRKDADYLGQLL---WNYCILDEGH 1582
+L +Y + D FD ++I S D R+ L L W+ ++DE H
Sbjct: 227 FALFDDERYAEAQHDAY---NPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAH 283
Query: 1583 II---KNSKSKITVAVKQLKAAH---RLILSGTPIQNNITDLWSLFDFLMPGFLGTERQF 1636
+ +++ S+ A++QL A H L+L+ TP Q ++ L P QF
Sbjct: 284 HLVWSEDAPSREYQAIEQL-AEHVPGVLLLTATPEQLGXESHFARLRLLDPNRFHDFAQF 342
Query: 1637 QATYGKPLVAARDSKCSAKDAEAGVLAMEAL 1667
V + + C DA A +LA L
Sbjct: 343 --------VEEQKNYCPVADAVAXLLAGNKL 365
>pdb|3OC3|A Chain A, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
pdb|3OC3|B Chain B, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
Length = 800
Score = 43.9 bits (102), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 511 ILSLDRFGDYVSDQVVAPVRETCAQALGAAFKYMHPSLVYETLYILLQMQRRPEWEIRHG 570
IL D+F D+V D+ VAPVR+ A L + + P+ + E L L +W+++
Sbjct: 226 ILVTDKFNDFVDDRTVAPVRDAAAYLLSRIYPLIGPNDIIEQLVGFLD---SGDWQVQFS 282
Query: 571 SLLGIKYL 578
L+ + YL
Sbjct: 283 GLIALGYL 290
>pdb|4JA0|A Chain A, Crystal Structure Of The Invertebrate Bi-functional Purine
Biosynthesis Enzyme Paics At 2.8 A Resolution
pdb|4JA0|B Chain B, Crystal Structure Of The Invertebrate Bi-functional Purine
Biosynthesis Enzyme Paics At 2.8 A Resolution
pdb|4JA0|C Chain C, Crystal Structure Of The Invertebrate Bi-functional Purine
Biosynthesis Enzyme Paics At 2.8 A Resolution
pdb|4JA0|D Chain D, Crystal Structure Of The Invertebrate Bi-functional Purine
Biosynthesis Enzyme Paics At 2.8 A Resolution
Length = 425
Score = 38.1 bits (87), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 1136 PSPNDKLIKNICSLTSMDP---CET---PQAAAMGSMEIIDDQDFLSFGSSTGKQKSRAH 1189
P P+DKL+++I S S+ C T P +AA+ + +II QD+L +G KQ AH
Sbjct: 352 PPPSDKLVQDIWSSLSVPSGLGCATVIYPDSAALMAAQIIGLQDYLVWGRLRSKQLDMAH 411
Query: 1190 MLAGGEDRSR 1199
L + + R
Sbjct: 412 SLRQADKKLR 421
>pdb|2HK7|A Chain A, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Mercury At 2.5 Angstrom
Resolution
pdb|2HK7|B Chain B, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Mercury At 2.5 Angstrom
Resolution
pdb|2HK8|A Chain A, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|B Chain B, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|C Chain C, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|D Chain D, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|E Chain E, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|F Chain F, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|G Chain G, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
pdb|2HK8|H Chain H, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus At 2.35 Angstrom Resolution
Length = 269
Score = 30.8 bits (68), Expect = 7.6, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 9/96 (9%)
Query: 1516 WAFEIEKFIDVSLMSTLQYVGSAQDRIALREQFDKHNVIITSYDVVRKDADYLGQLLWNY 1575
W EK I ++ L+ V S ++ I DK VI+ + V KD D ++NY
Sbjct: 152 WNRTKEKAIKLAQKFPLEVVNSPEEVI------DKVQVIVNTTSVGLKDED---PEIFNY 202
Query: 1576 CILDEGHIIKNSKSKITVAVKQLKAAHRLILSGTPI 1611
++ + H++ + K T +K+ K +L G P+
Sbjct: 203 DLIKKDHVVVDIIYKETKLLKKAKEKGAKLLDGLPM 238
>pdb|2HK9|A Chain A, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Shikimate And Nadp+ At 2.2
Angstrom Resolution
pdb|2HK9|B Chain B, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Shikimate And Nadp+ At 2.2
Angstrom Resolution
pdb|2HK9|C Chain C, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Shikimate And Nadp+ At 2.2
Angstrom Resolution
pdb|2HK9|D Chain D, Crystal Structure Of Shikimate Dehydrogenase From Aquifex
Aeolicus In Complex With Shikimate And Nadp+ At 2.2
Angstrom Resolution
Length = 275
Score = 30.8 bits (68), Expect = 7.6, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 9/96 (9%)
Query: 1516 WAFEIEKFIDVSLMSTLQYVGSAQDRIALREQFDKHNVIITSYDVVRKDADYLGQLLWNY 1575
W EK I ++ L+ V S ++ I DK VI+ + V KD D ++NY
Sbjct: 158 WNRTKEKAIKLAQKFPLEVVNSPEEVI------DKVQVIVNTTSVGLKDED---PEIFNY 208
Query: 1576 CILDEGHIIKNSKSKITVAVKQLKAAHRLILSGTPI 1611
++ + H++ + K T +K+ K +L G P+
Sbjct: 209 DLIKKDHVVVDIIYKETKLLKKAKEKGAKLLDGLPM 244
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 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 48,085,122
Number of Sequences: 62578
Number of extensions: 1900434
Number of successful extensions: 3961
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 3941
Number of HSP's gapped (non-prelim): 11
length of query: 1806
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1693
effective length of database: 7,902,023
effective search space: 13378124939
effective search space used: 13378124939
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: 59 (27.3 bits)