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= 035741
(890 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J7N|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
pdb|2J7N|B Chain B, Structure Of The Rnai Polymerase From Neurospora Crassa
pdb|2J7O|A Chain A, Structure Of The Rnai Polymerase From Neurospora Crassa
Length = 1022
Score = 63.5 bits (153), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 92/388 (23%), Positives = 151/388 (38%), Gaps = 88/388 (22%)
Query: 519 LMSSAENTNVLKELLNCGYKPDAEPFLSMMPQTFHASNLLELRTRARIFIQNGQAMMGCL 578
L S E T L L+N G+ P + +L + L+++ I + +
Sbjct: 487 LPDSQEET--LNFLMNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIA 544
Query: 579 DEKGTLEYGQ---GL------------------MVVAKKPCLHPGDMRVLRAVDVPALHH 617
D G LE + G ++VA+ P P D++ +RAV P LH
Sbjct: 545 DFWGVLEENEVHVGFSSKFRDEEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHS 604
Query: 618 MVDCVLFPAKGERPHTNECSGSDQDGEIYFVCWDHDRIPPLQFQPTAYTPAPEKILARD- 676
+ D ++F KG+ P + SG D DG++ +VCWD + + P + L +D
Sbjct: 605 LKDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDK 664
Query: 677 -------------------VTIEDVEEYFADYIVNDSLGIICNAHVVYAYSEPDKAMSNR 717
T + +++ F + + LG+ N Y + ++SN+
Sbjct: 665 TTFKQLMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCTNYKERLCYI--NNSVSNK 722
Query: 718 CPDLVKLSSIVG---DFSKTGVAATIPS--RLRVKI------YPDFMEKQDKTWY---ES 763
P ++ LSS+VG D SK G+ S +LR ++ PD M K D +W E
Sbjct: 723 -PAII-LSSLVGNLVDQSKQGIVFNEASWAQLRRELLGGALSLPDPMYKSD-SWLGRGEP 779
Query: 764 QHIVGNLY---------REVNGIAPSTTTIKSFAKEGAMQFYDTDME--VNGFKEV---- 808
HI+ L +E+ + K E F+D D+ FKE+
Sbjct: 780 THIIDYLKFSIARPAIDKELEAFHNAMKAAKD--TEDGAHFWDPDLASYYTFFKEISDKS 837
Query: 809 ---AMQFDGFKYRTEYDNKLGNLMDYYG 833
A+ F K N++G + YG
Sbjct: 838 RSSALLFTTLK------NRIGEVEKEYG 859
>pdb|1D4U|A Chain A, Interactions Of Human Nucleotide Excision Repair Protein
Xpa With Rpa70 And Dna: Chemical Shift Mapping And 15n
Nmr Relaxation Studies
Length = 111
Score = 32.7 bits (73), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 74 FLKASSAKRRTP---HFAKRTPHYKLGGDLKLNFGCQISKDKFSVFWSQENVS 123
LK ++R P K+ PH+ GD+KL QI K V+ SQE +
Sbjct: 52 LLKDCDLEKREPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALE 104
>pdb|1XPA|A Chain A, Solution Structure Of The Dna-And Rpa-Binding Domain Of
The Human Repair Factor Xpa, Nmr, 1 Structure
Length = 122
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 74 FLKASSAKRRTP---HFAKRTPHYKLGGDLKLNFGCQISKDKFSVFWSQE 120
LK ++R P K+ PH+ GD+KL QI K V+ SQE
Sbjct: 52 LLKDCDLEKREPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQE 101
>pdb|2OLC|A Chain A, Crystal Structure Of 5-Methylthioribose Kinase In Complex
With Adp-2ho
pdb|2OLC|B Chain B, Crystal Structure Of 5-Methylthioribose Kinase In Complex
With Adp-2ho
pdb|2PU8|A Chain A, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PU8|B Chain B, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUI|A Chain A, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUI|B Chain B, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUL|A Chain A, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUL|B Chain B, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUN|A Chain A, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUN|B Chain B, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUP|A Chain A, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
pdb|2PUP|B Chain B, Structures Of 5-Methylthioribose Kinase Reveal Substrate
Specificity And Unusual Mode Of Nucleotide Binding
Length = 397
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 400 AARLGQSFASSREAL-HVDSNIGKISAELAETVAKKCGYAIYTPSAFQI 447
AA+L +SF +S E L H D + G I A ET +A Y P F +
Sbjct: 215 AAKLKKSFLTSAETLIHGDLHTGSIFASEHETKVIDPEFAFYGPIGFDV 263
>pdb|1GR0|A Chain A, Myo-Inositol 1-Phosphate Synthase From Mycobacterium
Tuberculosis In Complex With Nad And Zinc
Length = 367
Score = 29.3 bits (64), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 11/83 (13%)
Query: 680 EDVEEYFADYIVNDSLGIICNAHVVYAYSEP---DKAMSNRCPDLVKLSSIVGDFSKTGV 736
E+ ++++A ++ + + NA V+ S+P K R P IVGD K+ V
Sbjct: 151 EEADKFYAQCAIDAGVAFV-NALPVFIASDPVWAKKFTDARVP-------IVGDDIKSQV 202
Query: 737 AATIPSRLRVKIYPDFMEKQDKT 759
ATI R+ K++ D + D+T
Sbjct: 203 GATITHRVLAKLFEDRGVQLDRT 225
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
0.320 0.135 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,717,682
Number of Sequences: 62578
Number of extensions: 1028901
Number of successful extensions: 2754
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2751
Number of HSP's gapped (non-prelim): 9
length of query: 890
length of database: 14,973,337
effective HSP length: 107
effective length of query: 783
effective length of database: 8,277,491
effective search space: 6481275453
effective search space used: 6481275453
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: 56 (26.2 bits)