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= 003070
(850 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PXI|A Chain A, Structure Of Meca108:clpc
pdb|3PXI|B Chain B, Structure Of Meca108:clpc
pdb|3PXI|C Chain C, Structure Of Meca108:clpc
Length = 758
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 512 FLLQGNDTIGKRRLALSIAESVFGSTDLLFHIDMRKRNDGVSSHSEMLMGTLKNYEKLVV 571
F+ G +GK LA ++AES+FG + + IDM + + S+ L ++ VV
Sbjct: 524 FIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHSTSGGQLTEKVRRKPYSVV 583
Query: 572 LVEDIDLADPQ----FIKILADGFETENFGKVI 600
L++ I+ A P +++L DG T++ G+ +
Sbjct: 584 LLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTV 616
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 67 PASVSKEDIKLVFEVFLRKKRRNTVIVGDCLSITDALVFDFMGRVERGDVPQELKQTHVI 126
P E+I+ V ++ LR+ + N V++G+ A+V R+ +GDVP+ LK ++
Sbjct: 171 PVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIV 230
Query: 127 KFHFA 131
Sbjct: 231 SLQMG 235
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 30/139 (21%), Positives = 61/139 (43%), Gaps = 23/139 (16%)
Query: 485 NVPWQFDSIHSIVEVLVECKSAKK-----ATWFLLQGNDTIGKRRLALSIAESVFGSTDL 539
V Q ++I ++ + + ++ K FL G +GK LA ++A ++F + +
Sbjct: 559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEA 618
Query: 540 LFHIDMRKRND------------GVSSHSE--MLMGTLKNYEKLVVLVEDIDLADPQ--- 582
+ IDM + + G + E L ++ V+L ++I+ A P
Sbjct: 619 MIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPDVFN 678
Query: 583 -FIKILADGFETENFGKVI 600
++IL DG T++ G+ +
Sbjct: 679 ILLQILDDGRLTDSHGRTV 697
>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium
Chloride And Adp
Length = 397
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 67 PASVSKEDIKLVFEVFLRKKRRNTVIVGDCLSITDALVFDFMGRVERGDVPQELKQTHVI 126
P E+I+ V ++ LR+ + N V++G+ A+V R+ +GDVP+ LK ++
Sbjct: 34 PVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIV 93
Query: 127 KFHFA 131
Sbjct: 94 SLQMG 98
>pdb|1JBK|A Chain A, Crystal Structure Of The First Nucelotide Binding Domain
Of Clpb
Length = 195
Score = 34.3 bits (77), Expect = 0.33, Method: Composition-based stats.
Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 3/105 (2%)
Query: 67 PASVSKEDIKLVFEVFLRKKRRNTVIVGDCLSITDALVFDFMGRVERGDVPQELKQTHVI 126
P E+I+ +V R+ + N V++G+ A+V R+ G+VP+ LK V+
Sbjct: 23 PVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL 82
Query: 127 KFHFAPVTLRFMKKEEVEMNLTELKRKVDSLTSVGGGAIIYTGDL 171
+ + E E LK ++ L G I++ +L
Sbjct: 83 ALDMGALVAGAKYRGEFE---ERLKGVLNDLAKQEGNVILFIDEL 124
>pdb|2DUM|A Chain A, Crystal Structure Of Hypothetical Protein, Ph0823
pdb|2DUM|B Chain B, Crystal Structure Of Hypothetical Protein, Ph0823
pdb|2DUM|C Chain C, Crystal Structure Of Hypothetical Protein, Ph0823
pdb|2DUM|D Chain D, Crystal Structure Of Hypothetical Protein, Ph0823
Length = 170
Score = 30.4 bits (67), Expect = 3.8, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 760 EIFKRQNKVNFS-------VEERVLEEVLIGSGFFHNSLFEKWLKEVFQTSLEAVXXXXX 812
E+F+++NK+ ++E LEE++ G FF+++ E LK++ + E
Sbjct: 23 EVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNA-EIELKDIKEKLKEEASRKLQ 81
Query: 813 XXXXEIRLCFGCKNDKVFANYG 834
E++ F KN + +G
Sbjct: 82 EKAEEVKRAFRAKNVRTIIRFG 103
>pdb|4FCT|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
pdb|4FD2|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb
pdb|4FD2|B Chain B, Crystal Structure Of The C-Terminal Domain Of Clpb
pdb|4FD2|D Chain D, Crystal Structure Of The C-Terminal Domain Of Clpb
Length = 308
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 31/144 (21%), Positives = 61/144 (42%), Gaps = 29/144 (20%)
Query: 483 QENVPWQFDSIHSIVEVLVECKSAKK-----ATWFLLQGNDTIGKRRLALSIAESVFGST 537
+ V Q ++I ++ + + ++ K FL G +GK LA ++A ++F +
Sbjct: 13 HKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTE 72
Query: 538 DLLFHIDMRKRNDGVSSHS-EMLMGTLKNYEKL----------------VVLVEDIDLAD 580
+ + IDM + + H+ L+G Y V+L + I+ A
Sbjct: 73 EAMIRIDM---TEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAH 129
Query: 581 PQ----FIKILADGFETENFGKVI 600
P ++IL DG T++ G+ +
Sbjct: 130 PDVFNILLQILDDGRLTDSHGRTV 153
>pdb|2P65|A Chain A, Crystal Structure Of The First Nucleotide Binding Domain
Of Chaperone Clpb1, Putative, (Pv089580) From Plasmodium
Vivax
Length = 187
Score = 30.4 bits (67), Expect = 4.6, Method: Composition-based stats.
Identities = 21/104 (20%), Positives = 44/104 (42%), Gaps = 12/104 (11%)
Query: 74 DIKLVFEVFLRKKRRNTVIVGDCLSITDALVFDFMGRVERGDVPQELKQTHVIKFHFAPV 133
+I+ ++ R+ + N +++GD A+V ++ +GDVP LK ++ + +
Sbjct: 30 EIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSL 89
Query: 134 TLRFMKKEEVEMNLTELKRKVDSL------------TSVGGGAI 165
+ + E L + ++V T VG GA+
Sbjct: 90 IAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAV 133
>pdb|4AMG|A Chain A, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AMG|B Chain B, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AN4|A Chain A, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AN4|B Chain B, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AN4|C Chain C, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AN4|D Chain D, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
Length = 400
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 565 NYEKLVVLVEDIDLADPQFIKILADGFETENFGKVIFVLTKG 606
NY KL V +D D+ DP + L +GF E F +V V G
Sbjct: 79 NYAKLFV-PDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDG 119
>pdb|4AMB|A Chain A, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
pdb|4AMB|B Chain B, Crystal Structure Of The Glycosyltransferase Snogd From
Streptomyces Nogalater
Length = 400
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 565 NYEKLVVLVEDIDLADPQFIKILADGFETENFGKVIFVLTKG 606
NY KL V +D D+ DP + L +GF E F +V V G
Sbjct: 79 NYAKLFV-PDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDG 119
>pdb|3IX1|A Chain A, Periplasmic
N-Formyl-4-Amino-5-Aminomethyl-2-Methylpyrimidine
Binding Protein From Bacillus Halodurans
pdb|3IX1|B Chain B, Periplasmic
N-Formyl-4-Amino-5-Aminomethyl-2-Methylpyrimidine
Binding Protein From Bacillus Halodurans
Length = 302
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 47/101 (46%), Gaps = 11/101 (10%)
Query: 552 VSSHSEMLMGTLKNYEKLVVLVED--------IDLADPQF--IKILADGFETENFGKVIF 601
VS ++ ++GT N+E V+ E +D P++ + ++++ E G+V+
Sbjct: 149 VSGRADAVVGTYINHEYPVLKHEGHDISYFNPVDYGVPEYDELVLISNEAYVEESGEVLA 208
Query: 602 VLTKGDSSNYEERIENQDSVINMTLKVNERNQNFDHKRKAE 642
+ YE +EN D +N+ L N+ NF ++ E
Sbjct: 209 AFWRAALKGYEWMVENPDEALNVLLT-NQDEANFPLIQEVE 248
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 0.130 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,799,891
Number of Sequences: 62578
Number of extensions: 872802
Number of successful extensions: 2352
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2345
Number of HSP's gapped (non-prelim): 13
length of query: 850
length of database: 14,973,337
effective HSP length: 107
effective length of query: 743
effective length of database: 8,277,491
effective search space: 6150175813
effective search space used: 6150175813
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: 56 (26.2 bits)