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= 029054
(200 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AJE|A Chain A, Crystal Structure Of S. Tokodaii Sua5 Complexed With
L-Threonine And Amppnp
Length = 352
Score = 30.0 bits (66), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 63 ILQDLTQEFYRLRSSLKAKQEHA-----SLLEDFREFDRTRLDLEDGVGSPEQALLKEHA 117
I ++L++EF L+ + E+ +L + FRE D+ +DL +G PE+ + A
Sbjct: 269 IPKELSKEFEGLQQIILGSDENLYEVARNLFDSFRELDKLNVDLGIMIGFPERGI--GFA 326
Query: 118 SINRS 122
+NR+
Sbjct: 327 IMNRA 331
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 30.0 bits (66), Expect = 0.82, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 54 SHTLTRHQEILQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ + + L LK E+ LLE R RTR DLE
Sbjct: 253 SHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLE 301
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 30.0 bits (66), Expect = 0.82, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 54 SHTLTRHQEILQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ + + L LK E+ LLE R RTR DLE
Sbjct: 247 SHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLE 295
>pdb|2EQA|A Chain A, Crystal Structure Of The Hypothetical Sua5 Protein From
Sulfolobus Tokodaii
pdb|4E1B|A Chain A, Re-Refinement Of Pdb Entry 2eqa - Sua5 Protein From
Sulfolobus Tokodaii With Bound
Threonylcarbamoyladenylate
Length = 352
Score = 30.0 bits (66), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 63 ILQDLTQEFYRLRSSLKAKQEHA-----SLLEDFREFDRTRLDLEDGVGSPEQAL 112
I ++L++EF L+ + E+ +L + FRE D+ +DL +G PE+ +
Sbjct: 269 IPKELSKEFEGLQQIILGSDENLYEVARNLFDSFRELDKLNVDLGIXIGFPERGI 323
>pdb|2BEZ|C Chain C, Structure Of A Proteolitically Resistant Core From The
Severe Acute Respiratory Syndrome Coronavirus S2 Fusion
Protein
Length = 77
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 124 GQMDSVISQAQATLGALVFQ-RSTFGGINSKLSNVSSRLPSV 164
G++ V++Q L LV Q S FG I+S L+++ SRL V
Sbjct: 33 GKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKV 74
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 28.1 bits (61), Expect = 3.1, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 54 SHTLTRHQEI---LQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ +Q++ QE + L+A+ LLE R RTR DLE
Sbjct: 272 SHFVTREEKMRLAIQNIEQELEERLAELRAQ---GKLLEAQRLEQRTRYDLE 320
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 54 SHTLTRHQEI---LQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ +Q++ QE + L+A+ LLE R RTR DLE
Sbjct: 247 SHFVTREEKMRLAIQNIEQELEERLAELRAQ---GKLLEAQRLEQRTRYDLE 295
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 54 SHTLTRHQEI---LQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ +Q++ QE + L+A+ LLE R RTR DLE
Sbjct: 247 SHFVTREEKMRLAIQNIEQELEERLAELRAQ---GKLLEAQRLEQRTRYDLE 295
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 54 SHTLTRHQEI---LQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ +Q++ QE + L+A+ LLE R RTR DLE
Sbjct: 246 SHFVTREEKMRLAIQNIEQELEERLAELRAQ---GKLLEAQRLEQRTRYDLE 294
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 28.1 bits (61), Expect = 3.4, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 54 SHTLTRHQEI---LQDLTQEFYRLRSSLKAKQEHASLLEDFREFDRTRLDLE 102
SH +TR +++ +Q++ QE + L+A+ LLE R RTR DLE
Sbjct: 247 SHFVTREEKMRLAIQNIEQELEERLAELRAQ---GKLLEAQRLEQRTRYDLE 295
>pdb|1WYY|A Chain A, Post-Fusion Hairpin Conformation Of The Sars Coronavirus
Spike Glycoprotein
pdb|1WYY|B Chain B, Post-Fusion Hairpin Conformation Of The Sars Coronavirus
Spike Glycoprotein
Length = 149
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 124 GQMDSVISQAQATLGALVFQ-RSTFGGINSKLSNVSSRLPSV 164
G++ V++Q L LV Q S FG I+S L+++ SRL V
Sbjct: 46 GKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKV 87
>pdb|4GBM|A Chain A, Sulfotransferase Domain From The Curacin Biosynthetic
Pathway
Length = 323
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 31/53 (58%)
Query: 131 SQAQATLGALVFQRSTFGGINSKLSNVSSRLPSVNQILSSIKRKKSMDTIILA 183
S A T + +S+ G +++ ++VSSRLP + ILSS + ++ ++LA
Sbjct: 1 SNASPTSLEIFATKSSPSGNSARPASVSSRLPGIIFILSSPRSGSTLLRVMLA 53
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
0.316 0.129 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,975,265
Number of Sequences: 62578
Number of extensions: 172873
Number of successful extensions: 485
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 473
Number of HSP's gapped (non-prelim): 19
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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: 49 (23.5 bits)