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= 035374
(66 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 48.5 bits (114), Expect = 8e-07, Method: Composition-based stats.
Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
KYG L+P Q+ D +L GD++DN+PGV+GIG+ A +L+ ++G L
Sbjct: 171 KYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSL 214
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 48.5 bits (114), Expect = 8e-07, Method: Composition-based stats.
Identities = 22/45 (48%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 12 KYGELKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
KYG L+P Q+ D +L GD++DN+PGV+GIG+ A +L+ ++G L
Sbjct: 171 KYG-LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSL 214
>pdb|1UT5|A Chain A, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT5|B Chain B, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease
pdb|1UT8|A Chain A, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
pdb|1UT8|B Chain B, Divalent Metal Ions (zinc) Bound To T5 5'-exonuclease
Length = 291
Score = 39.3 bits (90), Expect = 6e-04, Method: Composition-based stats.
Identities = 17/35 (48%), Positives = 24/35 (68%)
Query: 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
QF+ + +++GD DNI GVEGIG R +I +FG
Sbjct: 191 QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 225
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a
pdb|1XO1|B Chain B, T5 5'-Exonuclease Mutant K83a
Length = 291
Score = 39.3 bits (90), Expect = 6e-04, Method: Composition-based stats.
Identities = 17/35 (48%), Positives = 24/35 (68%)
Query: 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
QF+ + +++GD DNI GVEGIG R +I +FG
Sbjct: 191 QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFG 225
>pdb|1EXN|A Chain A, T5 5'-Exonuclease
pdb|1EXN|B Chain B, T5 5'-Exonuclease
Length = 290
Score = 38.9 bits (89), Expect = 8e-04, Method: Composition-based stats.
Identities = 17/35 (48%), Positives = 23/35 (65%)
Query: 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFG 54
QF+ + ++ GD DNI GVEGIG R +I +FG
Sbjct: 190 QFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFG 224
>pdb|4F3T|A Chain A, Human Argonaute-2 - Mir-20a Complex
Length = 861
Score = 29.3 bits (64), Expect = 0.57, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 2 ASFGMEDFARKYGELKPSQFVDVISLV----------GDKADNIPGVEGIGDVRAVQLIT 51
ASF + + R++G + + DV V +KA P V+G+ D+R Q T
Sbjct: 388 ASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATP-VQGVWDMRNKQFHT 446
Query: 52 KFGMLVFNVECFS 64
+ V+ + CF+
Sbjct: 447 GIEIKVWAIACFA 459
>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
pdb|3Q8M|B Chain B, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
In Complex With Substrate 5'-Flap Dna And K+
Length = 341
Score = 29.3 bits (64), Expect = 0.58, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52
L QFVD+ L+G +D + GIG RAV LI K
Sbjct: 217 LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQK 251
>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Product 5'-Flap Dna, Sm3+, And K+
pdb|3Q8L|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
Complex With Substrate 5'-Flap Dna, Sm3+, And K+
Length = 341
Score = 29.3 bits (64), Expect = 0.59, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52
L QFVD+ L+G +D + GIG RAV LI K
Sbjct: 217 LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQK 251
>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Y Chain Y, Crystal Structure Of The Human Fen1-Pcna Complex
pdb|1UL1|Z Chain Z, Crystal Structure Of The Human Fen1-Pcna Complex
Length = 379
Score = 29.3 bits (64), Expect = 0.62, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 LKPSQFVDVISLVGDKADNIPGVEGIGDVRAVQLITK 52
L QFVD+ L+G +D + GIG RAV LI K
Sbjct: 217 LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQK 251
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
Length = 346
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 20 QFVDVISLVGDKADNIPGVEGIGDVRAVQLITKFGML 56
Q +D+ L+G N G+ GIG RA+++I K+G +
Sbjct: 222 QLIDIGILIGTDY-NPDGIRGIGPERALKIIKKYGKI 257
>pdb|4EI1|A Chain A, Crystal Structure Of Human Argonaute2
pdb|4EI3|A Chain A, Crystal Structure Of Human Argonaute2
Length = 859
Score = 27.3 bits (59), Expect = 1.9, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 11/73 (15%)
Query: 2 ASFGMEDFARKYGELKPSQFVDVISLV----------GDKADNIPGVEGIGDVRAVQLIT 51
A F + + R++G + + DV V +KA P V+G+ D+R Q T
Sbjct: 386 ADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATP-VQGVWDMRNKQFHT 444
Query: 52 KFGMLVFNVECFS 64
+ V+ + CF+
Sbjct: 445 GIEIKVWAIACFA 457
>pdb|3HRD|A Chain A, Crystal Structure Of Nicotinate Dehydrogenase
pdb|3HRD|E Chain E, Crystal Structure Of Nicotinate Dehydrogenase
Length = 425
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 24 VISLVGDKADNIPGVEGIGDVRAVQLITKFGMLVFNVECF 63
++SL KA I GVE + D A+ +FG+++ + C
Sbjct: 51 IVSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCL 90
>pdb|4GSQ|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSR|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSU|A Chain A, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
pdb|4GSU|B Chain B, Structural Basis For The Inhibition Of Mycobacterium
Tuberculosis L,d- Transpeptidase By Meropenem, A Drug
Effective Against Extensively Drug-resistant Strains
Length = 287
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 13 YGELKPSQFVDVISLVGDKADNIPGVEGIGD 43
Y +K V+V++ VG +PG++G+GD
Sbjct: 237 YDHVKRGDIVEVVNTVGG---TLPGIDGLGD 264
>pdb|4HUC|A Chain A, Crystal Structure Of Ldtmt2, A L,D-Transpeptidase From
Mycobacterium Tuberculosis: Domain B And C
pdb|4HUC|B Chain B, Crystal Structure Of Ldtmt2, A L,D-Transpeptidase From
Mycobacterium Tuberculosis: Domain B And C
Length = 262
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 13 YGELKPSQFVDVISLVGDKADNIPGVEGIGD 43
Y +K V+V++ VG +PG++G+GD
Sbjct: 220 YDHVKRGDIVEVVNTVGG---TLPGIDGLGD 247
>pdb|3U1P|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3U1P|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3VAE|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
pdb|3VAE|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With Modified Catalytic Cysteine (C354)
Length = 287
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 13 YGELKPSQFVDVISLVGDKADNIPGVEGIGD 43
Y +K V+V++ VG +PG++G+GD
Sbjct: 245 YDHVKRGDIVEVVNTVGG---TLPGIDGLGD 272
>pdb|3TX4|A Chain A, Crystal Structure Of Mutant (C354a) M. Tuberculosis
Ld-Transpeptidase Type 2
pdb|3TX4|B Chain B, Crystal Structure Of Mutant (C354a) M. Tuberculosis
Ld-Transpeptidase Type 2
Length = 287
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 13 YGELKPSQFVDVISLVGDKADNIPGVEGIGD 43
Y +K V+V++ VG +PG++G+GD
Sbjct: 245 YDHVKRGDIVEVVNTVGG---TLPGIDGLGD 272
>pdb|3TUR|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 Complexed With A Peptidoglycan Fragment
pdb|3TUR|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 Complexed With A Peptidoglycan Fragment
pdb|3U1Q|A Chain A, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With 2- Mercaptoethanol
pdb|3U1Q|B Chain B, Crystal Structure Of M. Tuberculosis Ld-Transpeptidase
Type 2 With 2- Mercaptoethanol
Length = 287
Score = 25.8 bits (55), Expect = 5.9, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 13 YGELKPSQFVDVISLVGDKADNIPGVEGIGD 43
Y +K V+V++ VG +PG++G+GD
Sbjct: 245 YDHVKRGDIVEVVNTVGG---TLPGIDGLGD 272
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
0.323 0.142 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,842,400
Number of Sequences: 62578
Number of extensions: 55939
Number of successful extensions: 152
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 145
Number of HSP's gapped (non-prelim): 17
length of query: 66
length of database: 14,973,337
effective HSP length: 37
effective length of query: 29
effective length of database: 12,657,951
effective search space: 367080579
effective search space used: 367080579
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)