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= 042439
(766 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 = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 74/178 (41%), Gaps = 33/178 (18%)
Query: 394 SLVSFPEVALPS------KLRKIEICSCDALKSLPEAWMCDTNSSLEILMEEGIQXXXXX 447
+L P ALP+ +LR++ I +C L LPE + T++S E +Q
Sbjct: 133 TLARNPLRALPASIASLNRLRELSIRACPELTELPEP-LASTDASGEHQGLVNLQSL--- 188
Query: 448 XXXXXXLLEKLEIESCRSLTCIFSKNELPATLESLEVGNLP-----------PSLKSLHV 496
+LE RSL + + L+SL++ N P P L+ L +
Sbjct: 189 ---------RLEWTGIRSLPASIANLQ---NLKSLKIRNSPLSALGPAIHHLPKLEELDL 236
Query: 497 LSCSKLESIAERLDNNTSLETIDICYCGNLKNLPSGLHNLHQLQEISIGRCGNLESFP 554
C+ L + L+ + + C NL LP +H L QL+++ + C NL P
Sbjct: 237 RGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLP 294
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 50/163 (30%), Positives = 76/163 (46%), Gaps = 19/163 (11%)
Query: 455 LEKLEIESCRSLTCIFSKNELPATLESLEVGNLPPSLKSLHVLSC--SKLESIAERLDNN 512
L +L I +C LT ELP L S + L +L L + + S+ + N
Sbjct: 152 LRELSIRACPELT------ELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANL 205
Query: 513 TSLETIDICYCGNLKNLPSGLHNLHQLQEISIGRCGNLESFPE--GGLPCAKLSKLRIHG 570
+L+++ I L L +H+L +L+E+ + C L ++P GG A L +L +
Sbjct: 206 QNLKSLKI-RNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGR--APLKRLILKD 262
Query: 571 CERLEALPKGLHNLTSLQELTIGRG----VELPSLEEDGLPTN 609
C L LP +H LT L++L + RG LPSL LP N
Sbjct: 263 CSNLLTLPLDIHRLTQLEKLDL-RGCVNLSRLPSLIAQ-LPAN 303
Score = 33.5 bits (75), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 41/164 (25%), Positives = 69/164 (42%), Gaps = 30/164 (18%)
Query: 496 VLSCSKLESIAERLDNNTSLETIDICYCGNLKNLPSGLHNLHQLQEISIGRCGNLESFPE 555
+ + L + + LET+ + L+ LP+ + +L++L+E+SI C L PE
Sbjct: 110 TIDAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPE 168
Query: 556 GGLPCAKLSKLRIHGCERLEALPKGLHNLTSLQELTIGRGVELPSLEEDG---LPTNLHS 612
P A H +GL NL SL+ LE G LP ++ +
Sbjct: 169 ---PLASTDASGEH---------QGLVNLQSLR------------LEWTGIRSLPASIAN 204
Query: 613 LWIAGNMEIWKSTIE-WGRGFHRFSSLRQLRISGCDDDMVSFPP 655
L +++I S + G H L +L + GC + ++PP
Sbjct: 205 LQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGC-TALRNYPP 247
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 116 WLGDSSLP-------NLVTLKFENCDMCTALPSVGQLPSLKHLAVCGMSRVKRLGSEFYG 168
W G SLP NL +LK N + P++ LP L+ L + G + ++ F G
Sbjct: 192 WTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG 251
Query: 169 NDP 171
P
Sbjct: 252 RAP 254
>pdb|4FS7|A Chain A, Crystal Structure Of A Hypothetical Leucine Rich Repeat
Protein (Bacova_04585) From Bacteroides Ovatus Atcc 8483
At 1.19 A Resolution
Length = 394
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 37/114 (32%), Positives = 54/114 (47%), Gaps = 19/114 (16%)
Query: 473 NELPATLESLEVGNLPPSLKSLH---VLSCSKLESIAERLDNNTSLETIDICY--CGNLK 527
+E AT ESLE +LP S ++LH C KL+SI +L N + D C+ C L+
Sbjct: 155 DEAFATCESLEYVSLPDSXETLHNGLFSGCGKLKSI--KLPRNLKI-IRDYCFAECILLE 211
Query: 528 N--LPSGLHNL--HQLQEISIGRCGNLESFPEGGLPCAKLSKLRIHGCERLEAL 577
N P+ L+ L L + + +SF E L K +GC LE++
Sbjct: 212 NXEFPNSLYYLGDFALSKTGVKNIIIPDSFTE-------LGKSVFYGCTDLESI 258
>pdb|1S16|A Chain A, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
pdb|1S16|B Chain B, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
Length = 390
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 10/108 (9%)
Query: 507 ERLDNNTSLETIDICYCGNLKNLPSGLHNLHQLQEISIGRCGNLESFPEGGLPCAKLSKL 566
E +DN ++D G+ K + LH L+ I GR ++ PE G+P +L
Sbjct: 38 EVIDN-----SVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILC 92
Query: 567 RIHGCERLE----ALPKGLHNLTSLQELTIGRGVELPSLEEDGLPTNL 610
R+H + GLH + + + VE+ ++ DG N+
Sbjct: 93 RLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEV-NVRRDGQVYNI 139
>pdb|2JE5|A Chain A, Structural And Mechanistic Basis Of Penicillin Binding
Protein Inhibition By Lactivicins
pdb|2JE5|B Chain B, Structural And Mechanistic Basis Of Penicillin Binding
Protein Inhibition By Lactivicins
Length = 720
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 557 GLPCAKLSKLRIHGCERLEALPKGLHNLTSLQELTIGRGVELPSLEEDGLPTNLHSLWIA 616
G A K+R+ + E L + +++S+ E+T G + S+E D L T++ S I+
Sbjct: 7 GYGVALFDKVRV---PQTEELVNQVKDISSISEITYSDGTVIASIESDMLRTSISSEQIS 63
Query: 617 GNME 620
N++
Sbjct: 64 ENLK 67
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
0.319 0.137 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,545,681
Number of Sequences: 62578
Number of extensions: 912834
Number of successful extensions: 1809
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1790
Number of HSP's gapped (non-prelim): 18
length of query: 766
length of database: 14,973,337
effective HSP length: 106
effective length of query: 660
effective length of database: 8,340,069
effective search space: 5504445540
effective search space used: 5504445540
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)