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= 008449
(565 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 417 bits (1073), Expect = e-117, Method: Compositional matrix adjust.
Identities = 241/581 (41%), Positives = 357/581 (61%), Gaps = 34/581 (5%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKM 60
MPAKTVVFT+VRK+DG +FRW+S GEYIQMSGRAGRRG+D+RGI I+M+D+KMEP AK
Sbjct: 448 MPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKG 507
Query: 61 MLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLLRNSFYQFQADHAIPDLEKQAKVLEE 120
M+KG AD L+SAFHL YNM+LN +R E SPE +L +SF+QFQ ++P +EK+ L++
Sbjct: 508 MVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKK 567
Query: 121 ERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYCLPFLQPGRFVCIECTRGDDN 180
+ D + +E+E+++K Y+ + Q K ++DVR +V P L FLQPGR V I G DN
Sbjct: 568 DFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEISVN-GKDN 626
Query: 181 SPSFSTEDHQVTWGVVIEFEK------VKGVYEDDANKKPEDSNYTVNILTRCVVSKDGA 234
WG V++F K VY D +Y VN++ +
Sbjct: 627 ----------YGWGAVVDFAKRINKRNPSAVYTDH-------ESYIVNVVVNTMYIDSPV 669
Query: 235 G-----KKTLK--IVPLKESGEPLVVSVPIS--QIIKLSSARLPMPKDLLPLQTRENMLK 285
TL I P +E + + +PI+ I + + RL MPKD+ +E + K
Sbjct: 670 NLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGK 729
Query: 286 STSEFLARNASGLP-LDPEANMGIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQKLKV 344
S E R G+P LDP NM I + KL+++I+ L + + ++ S +E+
Sbjct: 730 SLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGK 789
Query: 345 LHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGYATSDDVVELKGKVACEIS 404
K +L +K +KR++ S + D+L+ RKRVLRRLG+ T +D++ELKG+VACEIS
Sbjct: 790 YSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEIS 849
Query: 405 SAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPREELELLFTQLQDTARR 464
S +EL LTELIFNG ++K E+ +LLSCF +QE+ ++A + + EL +++ A +
Sbjct: 850 SGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAK 909
Query: 465 VAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLE 524
+AK+ + K+++ + +V SFR ++ME VY W +G+ F +I ++T V+EGSLIR +RLE
Sbjct: 910 IAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLE 969
Query: 525 EVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVFAASLYL 565
E++++L+ A +IG + L+ K E + I RDIV A SLYL
Sbjct: 970 ELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL 1010
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 417 bits (1071), Expect = e-117, Method: Compositional matrix adjust.
Identities = 241/581 (41%), Positives = 357/581 (61%), Gaps = 34/581 (5%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKM 60
MPAKTVVFT+VRK+DG +FRW+S GEYIQMSGRAGRRG+D+RGI I+M+D+KMEP AK
Sbjct: 546 MPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKG 605
Query: 61 MLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLLRNSFYQFQADHAIPDLEKQAKVLEE 120
M+KG AD L+SAFHL YNM+LN +R E SPE +L +SF+QFQ ++P +EK+ L++
Sbjct: 606 MVKGQADRLDSAFHLGYNMILNLMRVEGISPEFMLEHSFFQFQNVISVPVMEKKLAELKK 665
Query: 121 ERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYCLPFLQPGRFVCIECTRGDDN 180
+ D + +E+E+++K Y+ + Q K ++DVR +V P L FLQPGR V I G DN
Sbjct: 666 DFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVTHPANALSFLQPGRLVEI-SVNGKDN 724
Query: 181 SPSFSTEDHQVTWGVVIEFEK------VKGVYEDDANKKPEDSNYTVNILTRCVVSKDGA 234
WG V++F K VY D +Y VN++ +
Sbjct: 725 ----------YGWGAVVDFAKRINKRNPSAVYTDH-------ESYIVNVVVNTMYIDSPV 767
Query: 235 G-----KKTLK--IVPLKESGEPLVVSVPIS--QIIKLSSARLPMPKDLLPLQTRENMLK 285
TL I P +E + + +PI+ I + + RL MPKD+ +E + K
Sbjct: 768 NLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSIKSIGNLRLYMPKDIRASGQKETVGK 827
Query: 286 STSEFLARNASGLP-LDPEANMGIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQKLKV 344
S E R G+P LDP NM I + KL+++I+ L + + ++ S +E+
Sbjct: 828 SLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMRLEELYGK 887
Query: 345 LHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGYATSDDVVELKGKVACEIS 404
K +L +K +KR++ S + D+L+ RKRVLRRLG+ T +D++ELKG+VACEIS
Sbjct: 888 YSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEIS 947
Query: 405 SAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPREELELLFTQLQDTARR 464
S +EL LTELIFNG ++K E+ +LLSCF +QE+ ++A + + EL +++ A +
Sbjct: 948 SGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAK 1007
Query: 465 VAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLE 524
+AK+ + K+++ + +V SFR ++ME VY W +G+ F +I ++T V+EGSLIR +RLE
Sbjct: 1008 IAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLE 1067
Query: 525 EVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVFAASLYL 565
E++++L+ A +IG + L+ K E + I RDIV A SLYL
Sbjct: 1068 ELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVSAGSLYL 1108
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 196 bits (497), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 174/593 (29%), Positives = 285/593 (48%), Gaps = 64/593 (10%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMV-DDKMEPSTAK 59
+P +TV+F+++RK DG+ R ++ GE+ QM+GRAGRRG+D G I+M + + +T K
Sbjct: 441 LPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFK 500
Query: 60 MMLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLLRNSFYQFQADHAIPDLEKQAKVLE 119
+ G L S F L+YNM+LN +R E E +++ SF + + P+ EKQ KVL+
Sbjct: 501 EVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQ 560
Query: 120 EERDSMVIEE----EDSLKNYYNLLQQYKSLKKDV-RDIVFSPKYCLPFLQPGRFVCIEC 174
EE ++ + ++ ++ + L+ YK ++ +++V SP L L+ GR V
Sbjct: 561 EELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPS-ILHILKEGRLV---- 615
Query: 175 TRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPED-SNYTVNILTRCVVSKDG 233
+F + + G V + V KP N N L DG
Sbjct: 616 --------AFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLI-YFPKADG 666
Query: 234 AGKKTLKIVPLKESGEPLVVSVPISQIIKLSSARLPMP------KDLLPLQ----TRENM 283
++ P + + + VP++ I ++ + P KD+ L N+
Sbjct: 667 YRRRNF---PKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNI 723
Query: 284 L--KSTSEFLARNASGLPLDPEANMGIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQK 341
L K+ E + GL + +Q L+ R + +F I K P + Q
Sbjct: 724 LDGKTLKEAINIEKQGLKI------------HQILLDRTNIRDEIFKLKSI-KCPNLSQH 770
Query: 342 LKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGYATSDDVVELKGKVAC 401
+ + KI+ + M S L+ + + R VL+ + + V LKG+VAC
Sbjct: 771 IVPKFKAHVIKKKIEELYHLM-SDQNLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVAC 829
Query: 402 EISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPREELELLFTQLQDT 461
EI+S EL LTELI + L + EE+V+LLS FV++ K ++ EE ++ +L
Sbjct: 830 EINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTRE-----EEPPIVTPRLAKG 884
Query: 462 ARRVAKV--QLECKVQI-------DVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVF 512
+R+ ++ ++ C D F++ R +M VY WA+G F EIME++P
Sbjct: 885 KQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEA 944
Query: 513 EGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVFAASLYL 565
EG+++R I L+E+ +++ A+ IG + L K A IKRDIVFAASLYL
Sbjct: 945 EGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL 997
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 42/138 (30%), Positives = 71/138 (51%), Gaps = 15/138 (10%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKM 60
+PA+ V+ ++ +FDG R I EY QM+GRAGR G+DERG I++V + K
Sbjct: 338 LPARRVIVRSLYRFDGYSKR-IKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKR 396
Query: 61 MLKGSADSLNSAF----HLSYNMLLNQIRCEEGSP-----ENLLRNSFYQFQADHAIP-D 110
+ G + + S HL ++ L I C+ + E+ ++F+ Q + ++ +
Sbjct: 397 YIFGEPERITSKLGVETHLRFHSL--SIICDGYAKTLEELEDFFADTFFFKQNEISLSYE 454
Query: 111 LEKQAKVLEEERDSMVIE 128
LE+ + LE MV+E
Sbjct: 455 LERVVRQLENW--GMVVE 470
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 3/55 (5%)
Query: 1 MPAKTVVFTNVRKFD---GDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52
+PA+TV+ ++ +F+ + I EY QMSGRAGR G D+ G I++V DK
Sbjct: 354 LPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDK 408
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSG--EYIQMSGRAGRRGIDERGICILM 48
+PA TV+ + + +K RW G + +QM GRAGR D +G IL+
Sbjct: 420 LPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILI 469
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 1 MPAKTVVFTNVRKFDGDKFRWISSG--EYIQMSGRAGRRGIDERGICILM 48
+PA TV+ + + +K RW G + +QM GRAGR D +G IL+
Sbjct: 420 LPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILI 469
>pdb|2GHI|A Chain A, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|B Chain B, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|C Chain C, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|D Chain D, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
Length = 260
Score = 32.0 bits (71), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 183 SFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDS-NYTVNILTRC-VVSKDGAGKKTL 239
SFS H+ +GV IEF V Y N + S N+ + T C +V G+GK T+
Sbjct: 4 SFSLTSHEKKFGVNIEFSDVNFSYPKQTNHRTLKSINFFIPSGTTCALVGHTGSGKSTI 62
>pdb|1X18|E Chain E, Contact Sites Of Era Gtpase On The Thermus Thermophilus
30s Subunit
Length = 231
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 296 SGLPLDPEANMGIRSSSYQKL--VRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTA 353
+G+P + +G ++++ + V R+E LE+LF EI + P EQ+L L Q+ +
Sbjct: 82 AGMPYVNQRWLGGMLTNFKTIQRVHRLEELEALFASPEIEERPKKEQRLHELERLQKYLS 141
Query: 354 KIKSIKR 360
+ +KR
Sbjct: 142 GFRLLKR 148
>pdb|1LPJ|A Chain A, Human Crbp Iv
Length = 133
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 29/70 (41%)
Query: 104 ADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYCLPF 163
A I L K KV+E+ DS I SL+NY+ + + +D R + L
Sbjct: 28 ATRKIAKLLKPQKVIEQNGDSFTIHTNSSLRNYFVKFKVGEEFDEDNRGLDNRKCKSLVI 87
Query: 164 LQPGRFVCIE 173
R CI+
Sbjct: 88 WDNDRLTCIQ 97
>pdb|1ZQ1|C Chain C, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
pdb|1ZQ1|D Chain D, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
Length = 633
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 372 DELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIF 416
D L+A K+V R LG D V +KG EI +EL + +I
Sbjct: 211 DALRATKKVKRGLGTIRQDLNVSIKGGARIEIKGVQELDMIPIII 255
>pdb|4ADZ|A Chain A, Crystal Structure Of The Apo Form Of A Copper-Sensitive
Operon Regulator (Csor) Protein From Streptomyces
Lividans
pdb|4ADZ|B Chain B, Crystal Structure Of The Apo Form Of A Copper-Sensitive
Operon Regulator (Csor) Protein From Streptomyces
Lividans
Length = 136
Score = 29.3 bits (64), Expect = 6.4, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 519 AIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKR 555
A++ LEE L+ + A G TE++AK EEA I R
Sbjct: 96 ALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGR 132
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
0.317 0.133 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,389,798
Number of Sequences: 62578
Number of extensions: 630838
Number of successful extensions: 1853
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1830
Number of HSP's gapped (non-prelim): 28
length of query: 565
length of database: 14,973,337
effective HSP length: 104
effective length of query: 461
effective length of database: 8,465,225
effective search space: 3902468725
effective search space used: 3902468725
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: 54 (25.4 bits)