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= 037904
(189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 40/130 (30%), Positives = 54/130 (41%), Gaps = 15/130 (11%)
Query: 16 FPQEPGNCSRLWEEADTLWEVLSDGTDIKE-PLSIELLFGLVQLTLNGCKNLEHLPRTIS 74
PQ P RL L D + E P + + GL LTL L LP +I+
Sbjct: 93 LPQFPDQAFRL----SHLQHXTIDAAGLXELPDTXQQFAGLETLTL-ARNPLRALPASIA 147
Query: 75 ALKYLSTLNLSGLLKFREFPEKTSSRD---------ELLEIHLEGTAIRGLPASIELLFG 125
+L L L++ + E PE +S D L + LE T IR LPASI L
Sbjct: 148 SLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQN 207
Query: 126 NAAPNLKNVP 135
+ ++N P
Sbjct: 208 LKSLKIRNSP 217
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 17/31 (54%)
Query: 46 PLSIELLFGLVQLTLNGCKNLEHLPRTISAL 76
PL I L L +L L GC NL LP I+ L
Sbjct: 270 PLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
>pdb|3BT7|A Chain A, Structure Of E. Coli 5-Methyluridine Methyltransferase
Trma In Complex With 19 Nucleotide T-Arm Analogue
pdb|3BT7|B Chain B, Structure Of E. Coli 5-Methyluridine Methyltransferase
Trma In Complex With 19 Nucleotide T-Arm Analogue
Length = 369
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 37/161 (22%), Positives = 63/161 (39%), Gaps = 30/161 (18%)
Query: 25 RLWEEADTLWEVLSDGTDIKE------PLSIELLFGLVQLTLNGCKNLEHLPRTISALKY 78
R+W + D L+ ++ D P + EL+ L+ + G +N L + + Y
Sbjct: 54 RIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDY 113
Query: 79 LSTLN---LSGLLKFREF-----PEKTSSRDEL----LEIHLEGTAIRG----------- 115
L+TL+ + LL ++ E + RD L L +HL G A +
Sbjct: 114 LTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDE 173
Query: 116 -LPASIELLFGNAAPNLKNVPETLGNVESLEVRLSCHKRAK 155
LP + + + N P N++ LE L K +K
Sbjct: 174 RLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSK 214
>pdb|1KF6|C Chain C, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1KF6|O Chain O, E. Coli Quinol-Fumarate Reductase With Bound Inhibitor
Hqno
pdb|1KFY|C Chain C, Quinol-fumarate Reductase With Quinol Inhibitor
2-[1-(4-chloro- Phenyl)-ethyl]-4,6-dinitro-phenol
pdb|1KFY|O Chain O, Quinol-fumarate Reductase With Quinol Inhibitor
2-[1-(4-chloro- Phenyl)-ethyl]-4,6-dinitro-phenol
pdb|1L0V|C Chain C, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|1L0V|O Chain O, Quinol-Fumarate Reductase With Menaquinol Molecules
pdb|2B76|C Chain C, E. Coli Quinol Fumarate Reductase Frda E49q Mutation
pdb|2B76|O Chain O, E. Coli Quinol Fumarate Reductase Frda E49q Mutation
pdb|3CIR|C Chain C, E. Coli Quinol Fumarate Reductase Frda T234a Mutation
pdb|3CIR|O Chain O, E. Coli Quinol Fumarate Reductase Frda T234a Mutation
pdb|3P4R|C Chain C, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With Glutarate
pdb|3P4R|O Chain O, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With Glutarate
pdb|3P4P|C Chain C, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With Fumarate
pdb|3P4P|O Chain O, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With Fumarate
pdb|3P4Q|C Chain C, Crystal Structure Of Menaquinol:oxidoreductase In Complex
With Oxaloacetate
pdb|3P4Q|O Chain O, Crystal Structure Of Menaquinol:oxidoreductase In Complex
With Oxaloacetate
pdb|3P4S|C Chain C, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With A 3-Nitropropionate Adduct
pdb|3P4S|O Chain O, Crystal Structure Of Menaquinol:fumarate Oxidoreductase In
Complex With A 3-Nitropropionate Adduct
Length = 130
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 109 EGTAIRGLPASIELLFGNAAPNLKNVPETL-GNVESLE 145
EGTA+ + SIEL+FG A LKN PE G V+ L+
Sbjct: 29 EGTAVPAVWFSIELIFGLFA--LKNGPEAWAGFVDFLQ 64
>pdb|3KLF|B Chain B, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|F Chain F, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|J Chain J, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|N Chain N, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
Length = 444
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 104 LEIHLEG--TAIRGLPASIELLFGNAAPNLKNVPETLGNVESL-EVRLSCHKRAKM---- 156
LE+ +G + I +P ++L G P +K P T +++L E+ K K+
Sbjct: 10 LEVLFQGPISPIETVP--VKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG 67
Query: 157 -QNDFDC-VEQIAKKDSDSWKKNVD 179
+N ++ V I KKDS W+K VD
Sbjct: 68 PENPYNTPVFAIKKKDSTKWRKLVD 92
>pdb|2QLU|A Chain A, Crystal Structure Of Activin Receptor Type Ii Kinase
Domain From Human
Length = 314
Score = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 139 GNVESLEV----RLSCHKRAKMQNDFDCVEQIAKKDSDSWK 175
G+++ LE+ R C +A++ NDF V+ +D SW+
Sbjct: 15 GSLQLLEIKARGRFGCVWKAQLMNDFVAVKIFPLQDKQSWQ 55
>pdb|2ZKR|NN Chain n, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 297
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 142 ESLEVRLSCHKRAKM-QNDFDCVEQIAKKDSDSWKKNVDEGIKLSAT 187
ES E H++ M QN D + + ++D D++KK + IK S T
Sbjct: 186 ESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVT 232
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
0.315 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,605,808
Number of Sequences: 62578
Number of extensions: 208283
Number of successful extensions: 569
Number of sequences better than 100.0: 118
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 117
Number of HSP's that attempted gapping in prelim test: 567
Number of HSP's gapped (non-prelim): 119
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)