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= psy11213
(621 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F9V|A Chain A, Crystal Structure Of A Near Full-Length Archaeal Mcm:
Functional Insights For An Aaa+ Hexameric Helicase
Length = 595
Score = 210 bits (534), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 108/227 (47%), Positives = 151/227 (66%), Gaps = 6/227 (2%)
Query: 367 QGNINICLMGDPGVAKSQLLSYIERLARRSQYTTGRGSSGVGLTAAVMKDPITNEMVLEG 426
+G+I+I ++GDPG AKSQ+L +I R+A R+ YTTG+GS+ GLTAAV+++ T E LE
Sbjct: 325 RGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEA 384
Query: 427 GALVLADQGICCIDEFDKLPDADRTAIHEVMEQQTISIAKAGIMTRLNARVSILAAANPA 486
GALVLAD GI IDE DK+ D DR AIHE MEQQT+SIAKAGI+ +LNAR +++AA NP
Sbjct: 385 GALVLADGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPK 444
Query: 487 YGRYNPKRSIEQNIQLPAALLSRFDLLWLIQDKPDRDNDLKLAQHITYVHKHSRQPPTEL 546
+GRY +R + NI LP +LSRFDL+++++D+P + D +LA +I VH +
Sbjct: 445 FGRYISERPVSDNINLPPTILSRFDLIFILKDQPG-EQDRELANYILDVHSGK----STK 499
Query: 547 KPIDMSLVRRYIDLC-KGKNPTVPSSLTEHIVKAYTELRKVARNSRD 592
ID+ +R+YI K P + S I + E+RK + + D
Sbjct: 500 NIIDIDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPD 546
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 67/272 (24%), Positives = 117/272 (43%), Gaps = 45/272 (16%)
Query: 86 IDLDDEFLIEFVKIDKDDNKIFKYSKQLSKLAHREQVAIYIDLDDVEEFNSDLATNIQNN 145
ID D F IEF+ K +N KY +++++L + ++ I+ DV FN +LA I NN
Sbjct: 2 IDYRDVF-IEFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLSFNENLAYEIINN 60
Query: 146 TRRYVQMFSELIFELLPDYKSHDVIAKDPLDIYIEHRLLLEQRNHPNPQELRNSQNRYPQ 205
T+ +I +L ++ DP Y +
Sbjct: 61 TK--------IILPILEGALYDHILQLDPT---------------------------YQR 85
Query: 206 DLMR-RFEVYFVPPSSGKPTPIREVKATHIGKLVNVRGVVTRSTEVKPLMTVATYTCDM- 263
D+ + + +P + +R++++T IGKL+ + G++ + T VK + ATY
Sbjct: 86 DIEKVHVRIVGIP----RVIELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIHP 141
Query: 264 -CGAETYQPISSLSFTPLLMCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHSDQVP 322
C E P +L P+ C G+ L +K + +Q+ +QE ++VP
Sbjct: 142 DCMQEFEWP-EDEEMPEVLEMPT-ICPKCGKPGQFRLIPEKTKLIDWQKAVIQERPEEVP 199
Query: 323 VGNIPRGITVLCRGENTRQVVPGDHVSVSGIF 354
G +PR + ++ + PGD V V+GI
Sbjct: 200 SGQLPRQLEIILEDDLVDSARPGDRVKVTGIL 231
>pdb|2VL6|A Chain A, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
pdb|2VL6|B Chain B, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
pdb|2VL6|C Chain C, Structural Analysis Of The Sulfolobus Solfataricus Mcm
Protein N-Terminal Domain
Length = 268
Score = 70.1 bits (170), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 71/273 (26%), Positives = 117/273 (42%), Gaps = 47/273 (17%)
Query: 86 IDLDDEFLIEFVKIDKDDNKIFKYSKQLSKLAHREQVAIYIDLDDVEEFNSDLATNIQNN 145
ID D F IEF+ K +N KY +++++L + ++ I+ DV FN +LA I NN
Sbjct: 8 IDYRDVF-IEFLTTFKGNNNQNKYIERINELVAYRKKSLIIEFSDVLSFNENLAYEIINN 66
Query: 146 TRRYVQMFSELIFELLPDYKSHDVIAKDPLDIYIEHRLLLEQRNHPNPQELRNSQNRYPQ 205
T+ +I +L ++ DP Y +
Sbjct: 67 TK--------IILPILEGALYDHILQLDPT---------------------------YQR 91
Query: 206 DLMRRFEVYFVPPSSGKPTPI--REVKATHIGKLVNVRGVVTRSTEVKPLMTVATYTCDM 263
D+ + V V G P I R++++T IGKL+ + G++ + T VK + ATY
Sbjct: 92 DI-EKVHVRIV----GIPRVIELRKIRSTDIGKLITIDGILVKVTPVKERIYKATYKHIH 146
Query: 264 --CGAETYQPISSLSFTPLLMCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEHSDQV 321
C E P +L P+ C G+ L +K + +Q+ +QE ++V
Sbjct: 147 PDCMQEFEWP-EDEEMPEVLEMPT-ICPKCGKPGQFRLIPEKTKLIDWQKAVIQERPEEV 204
Query: 322 PVGNIPRGITVLCRGENTRQVVPGDHVSVSGIF 354
P G +PR + ++ + PGD V V+GI
Sbjct: 205 PSGQLPRQLEIILEDDLVDSARPGDRVKVTGIL 237
>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 51/152 (33%), Positives = 72/152 (47%), Gaps = 9/152 (5%)
Query: 369 NINICLMGDPGVAKSQLLSYIERLARRSQYTTGRGSSGVGLTAAVMKDPITNEMVLEGGA 428
+++ L G P V L ++ LA R Y R + LTA + +D L GA
Sbjct: 239 RLHVLLAGYPVVCSEILHHVLDHLAPRGVYVDLRRTELTDLTAVLKED---RGWALRAGA 295
Query: 429 LVLADQGICCIDEFDKLPDADRTAIHEVMEQQTISIAKAGIMTRLNARVSILAAANPAYG 488
VLAD GI +D + P+ R A+ E M++ T+++ GI LNAR ++LAA NP G
Sbjct: 296 AVLADGGILAVDHLEGAPEPHRWALMEAMDKGTVTVD--GIA--LNARCAVLAAINP--G 349
Query: 489 RYNPKRSIEQNIQLPAALLSRFDLLWLIQDKP 520
P I L LS FDL+ + P
Sbjct: 350 EQWPSDPPIARIDLDQDFLSHFDLIAFLGVDP 381
>pdb|1LTL|A Chain A, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|B Chain B, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|C Chain C, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|D Chain D, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|E Chain E, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|F Chain F, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
Length = 279
Score = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 60/212 (28%), Positives = 98/212 (46%), Gaps = 22/212 (10%)
Query: 150 VQMFSELIFELLPDYKSHDVIAKDPLDIYIEH----RLLLEQRN---HPNPQELRN-SQN 201
+Q + + +FE + Y + I D LD+ + LL+E+ + Q +RN +
Sbjct: 24 LQDYKDRVFEAIEKYPNVRSIEVDYLDLEMFDPDLADLLIEKPDDVIRAAQQAIRNIDRL 83
Query: 202 RYPQDLMRRFEVYFVPPSSGKPTPIREVKATHIGKLVNVRGVVTRSTEVKPLMTVATYTC 261
R DL RF P+RE+++ IGK V V G+V ++ E++P + A + C
Sbjct: 84 RKNVDLNIRF------SGISNVIPLRELRSKFIGKFVAVDGIVRKTDEIRPRIVKAVFEC 137
Query: 262 DMCGAETYQPISSLSFTPLLMCPSEDCQVNKSGGRLY-LQTRGSKFVKFQELKVQEHSDQ 320
C S+ T +C ++ GGR + L S+F+ Q LK+QE +
Sbjct: 138 RGCMRHHAVTQSTNMITEPSLC-------SECGGRSFRLLQDESEFLDTQTLKLQEPLEN 190
Query: 321 VPVGNIPRGITVLCRGENTRQVVPGDHVSVSG 352
+ G PR ITV+ + + PGD V V+G
Sbjct: 191 LSGGEQPRQITVVLEDDLVDTLTPGDIVRVTG 222
>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
Length = 368
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 30/134 (22%), Positives = 54/134 (40%), Gaps = 22/134 (16%)
Query: 364 QVTQGNINICLMGDPGVAKSQLLSYIERLARRSQYTTGRGSSGVGLTAAVM--------- 414
++ + + + G+ G K E +AR +GR + V L A +
Sbjct: 147 KIAKSKAPVLITGESGTGK-------EIVARLIHRYSGRKGAFVDLNCASIPQELAESEL 199
Query: 415 ----KDPITNEMVLEGGALVLADQGICCIDEFDKLPDADRTAIHEVMEQQTISIAKAGIM 470
K T + + G L LADQG +DE +L + + V+E T S + G
Sbjct: 200 FGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELDQRVQAKLLRVLE--TGSFTRLGGN 257
Query: 471 TRLNARVSILAAAN 484
++ + +++A N
Sbjct: 258 QKIEVDIRVISATN 271
>pdb|3F3P|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|I Chain I, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|J Chain J, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
Length = 351
Score = 32.7 bits (73), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 105 KIFKYSKQLSKLAHREQVAIYIDLDDVEEFNSDLATNIQNNTRRYVQMFSELIFELLPDY 164
+IFK +++LS LA E + D+ + + D +NT ++ S L ELL ++
Sbjct: 243 RIFKITEKLSPLASEESLTNSNXFDNSADVDXDAQGRSDSNTEEKAELQSNLQVELLSEH 302
Query: 165 KSHD 168
H+
Sbjct: 303 DDHN 306
>pdb|3F3F|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3G|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
Length = 351
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 105 KIFKYSKQLSKLAHREQVAIYIDLDDVEEFNSDLATNIQNNTRRYVQMFSELIFELLPDY 164
+IFK +++LS LA E + D+ + + D +NT ++ S L ELL ++
Sbjct: 243 RIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLSEH 302
Query: 165 KSHD 168
H+
Sbjct: 303 DDHN 306
>pdb|3EWE|A Chain A, Crystal Structure Of The Nup85SEH1 COMPLEX
pdb|3EWE|C Chain C, Crystal Structure Of The Nup85SEH1 COMPLEX
Length = 349
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 105 KIFKYSKQLSKLAHREQVAIYIDLDDVEEFNSDLATNIQNNTRRYVQMFSELIFELLPDY 164
+IFK +++LS LA E + D+ + + D +NT ++ S L ELL ++
Sbjct: 241 RIFKITEKLSPLASEESLTNSNMFDNSADVDMDAQGRSDSNTEEKAELQSNLQVELLSEH 300
Query: 165 KSHD 168
H+
Sbjct: 301 DDHN 304
>pdb|3T0Q|A Chain A, Motor Domain Structure Of The Kar3-Like Kinesin From
Ashbya Gossypii
Length = 349
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 149 YVQMFSELIFELLPDYKSHDVI 170
Y+++++E I +LL D+KSHD I
Sbjct: 138 YIEIYNETILDLLRDFKSHDNI 159
>pdb|2ING|X Chain X, X-Ray Structure Of The Brca1 Brct Mutant M1775k
Length = 213
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 184 LLEQRNHPNPQELRNSQNRYPQDLMRRFEVYFVPPSSGKPTPIREVKATHIG-KLVNVRG 242
++ RNH P+ R SQ+R + R E+ P + KPT E G +V
Sbjct: 94 VVNGRNHQGPKRARESQDR---KIFRGLEICCYGPFTNKPTDQLEWMVQLCGASVVKELS 150
Query: 243 VVTRSTEVKPLMTV 256
T T V P++ V
Sbjct: 151 SFTLGTGVHPIVVV 164
>pdb|3EOL|A Chain A, 2.0a Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis (P43212)
pdb|3EOL|B Chain B, 2.0a Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis (P43212)
Length = 433
Score = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 22/55 (40%)
Query: 482 AANPAYGRYNPKRSIEQNIQLPAALLSRFDLLWLIQDKPDRDNDLKLAQHITYVH 536
A A G Y K IE I A DL+W+ KPD + A+ + H
Sbjct: 251 AGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAH 305
>pdb|3E5B|A Chain A, 2.4 A Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis
pdb|3E5B|B Chain B, 2.4 A Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis
pdb|3E5B|C Chain C, 2.4 A Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis
pdb|3E5B|D Chain D, 2.4 A Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis
pdb|3OQ8|A Chain A, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To The Product Mimic Malonate
pdb|3OQ8|B Chain B, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To The Product Mimic Malonate
pdb|3OQ8|C Chain C, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To The Product Mimic Malonate
pdb|3OQ8|D Chain D, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To The Product Mimic Malonate
pdb|3P0X|A Chain A, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To Magnesium Isocitrate
pdb|3P0X|B Chain B, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To Magnesium Isocitrate
pdb|3P0X|C Chain C, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To Magnesium Isocitrate
pdb|3P0X|D Chain D, Crystal Structure Of Isocitrate Lyase From Brucella
Melitensis, Bound To Magnesium Isocitrate
Length = 433
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 22/55 (40%)
Query: 482 AANPAYGRYNPKRSIEQNIQLPAALLSRFDLLWLIQDKPDRDNDLKLAQHITYVH 536
A A G Y K IE I A DL+W+ KPD + A+ + H
Sbjct: 251 AGRTAEGFYQVKNGIEPCIARAIAYAPYCDLIWMETSKPDLAQARRFAEAVHKAH 305
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
0.321 0.136 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,347,410
Number of Sequences: 62578
Number of extensions: 731038
Number of successful extensions: 1910
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1895
Number of HSP's gapped (non-prelim): 18
length of query: 621
length of database: 14,973,337
effective HSP length: 105
effective length of query: 516
effective length of database: 8,402,647
effective search space: 4335765852
effective search space used: 4335765852
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: 54 (25.4 bits)