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= psy2640
(613 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 = 139 bits (350), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 95/290 (32%), Positives = 139/290 (47%), Gaps = 82/290 (28%)
Query: 85 SVYVCGNXXXXXXXXXXXXREGG-GDFALEAGALVLADQGVCCIDEFDKMSAQHQNGMLY 143
+VY G RE G G++ LEAGALVLAD G+ IDE DKM + +
Sbjct: 354 AVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALVLADGGIAVIDEIDKMRDEDR----- 408
Query: 144 TAKAMRGITSRQYTPAFITMSIHPVMGEKRHTMSAQHQALLEAMEQQSISIAKASVVCSL 203
++IH EAMEQQ++SIAKA +V L
Sbjct: 409 -------------------VAIH------------------EAMEQQTVSIAKAGIVAKL 431
Query: 204 PARTSVIAAANPVGGHYNRAKTVAENLRMGQALLSRFDLVFILLDNPDEHLDTLLSEHVM 263
AR +VIAA NP G Y + V++N+ + +LSRFDL+FIL D P E D L+ +++
Sbjct: 432 NARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGEQ-DRELANYIL 490
Query: 264 ASLSGFQSNRNPSHSTQSFTENPNSVQSDIPLSERLKPGPGEELPLIPAPLLHKYLAYAR 323
SG +S +N +I L KY+AYAR
Sbjct: 491 DVHSG-KSTKN----------------------------------IIDIDTLRKYIAYAR 515
Query: 324 KYVSKPELSTEAALLLQEFYLNLRKHHHSVDATP--VTTRQLESLVRLTQ 371
KYV+ P++++EA L+ +F++ +RK +P +T RQLE+L+R+++
Sbjct: 516 KYVT-PKITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRISE 564
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 38/94 (40%), Positives = 52/94 (55%), Gaps = 16/94 (17%)
Query: 371 QDIQAEPNLFKLLVNSLCPSIFGHEMVKAGLLLALFGGCHST---NGSRGDAHVLIVGDP 427
+D+ +P + +++S+ PSI+GH +K L LALFGG RGD H+LI+GDP
Sbjct: 277 KDLAKDPWIRDRIISSIAPSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDP 336
Query: 428 GLGKSQMLHACCAAKKFISVLQKKAEVQSRSVFT 461
G KSQML FIS V R+V+T
Sbjct: 337 GTAKSQMLQ-------FIS------RVAPRAVYT 357
>pdb|3F8T|A Chain A, Crystal Structure Analysis Of A Full-Length Mcm Homolog
From Methanopyrus Kandleri
Length = 506
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 63/267 (23%), Positives = 95/267 (35%), Gaps = 100/267 (37%)
Query: 110 FALEAGALVLADQGVCCIDEFDKMSAQHQNGMLYTAKAMRGITSRQYTPAFITMSIHPVM 169
+AL AGA VLAD G+ +D + H+
Sbjct: 289 WALRAGAAVLADGGILAVDHLEGAPEPHR------------------------------- 317
Query: 170 GEKRHTMSAQHQALLEAMEQQSISIAKASVVCSLPARTSVIAAANPVGGHYNRAKTVAEN 229
AL+EAM++ ++++ +L AR +V+AA NP G + +A
Sbjct: 318 -----------WALMEAMDKGTVTVDG----IALNARCAVLAAINP-GEQWPSDPPIA-R 360
Query: 230 LRMGQALLSRFDLVFILLDNPDEHLDTLLSEHVMASLSGFQSNRNPSHSTQSFTENPNSV 289
+ + Q LS FDL+ L +P P + TE P+
Sbjct: 361 IDLDQDFLSHFDLIAFLGVDP-----------------------RPGEPEEQDTEVPSYT 397
Query: 290 QSDIPLSERLKPGPGEELPLIPAPLLHKYLAYARKYVSKPELSTEAALLLQEFYLNLRKH 349
LL +YL YA + PEL+ EA L+ +Y R+
Sbjct: 398 ------------------------LLRRYLLYAIREHPAPELTEEARKRLEHWYETRREE 433
Query: 350 HH-----SVDATPVTTRQLESLVRLTQ 371
+ PVT RQLES+ RL +
Sbjct: 434 VEERLGMGLPTLPVTRRQLESVERLAK 460
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 32.0 bits (71), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLGK+ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 73
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLGK+ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 73
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLGK+ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 73
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLGK+ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 73
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLGK+ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS 73
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 392 FGHEMVKAGLLLALFGGCHSTNGSRGDA--HVLIVGDPGLGKSQMLHACCA 440
G E VK L LAL RG+ HVL+ G PGLG++ + H +
Sbjct: 28 IGQENVKKKLSLAL-----EAAKMRGEVLDHVLLAGPPGLGRTTLAHIIAS 73
>pdb|1MKM|A Chain A, Crystal Structure Of The Thermotoga Maritima Iclr
pdb|1MKM|B Chain B, Crystal Structure Of The Thermotoga Maritima Iclr
Length = 249
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 467 QLATSANISVDNFFTFLTSLNDQGFLLKKGKQLY 500
++A N+SV N + ++ L ++GF+L+K + Y
Sbjct: 28 EIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRY 61
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 531 QLATSANISVDNFFTFLTSLNDQGFLLKKGKQLY 564
++A N+SV N + ++ L ++GF+L+K + Y
Sbjct: 28 EIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRY 61
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 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,466,544
Number of Sequences: 62578
Number of extensions: 608841
Number of successful extensions: 1707
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1696
Number of HSP's gapped (non-prelim): 16
length of query: 613
length of database: 14,973,337
effective HSP length: 105
effective length of query: 508
effective length of database: 8,402,647
effective search space: 4268544676
effective search space used: 4268544676
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)