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= 026996
(229 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C8U|A Chain A, Crystal Structure Of Putative Fructose Transport System
Kinase (Yp_612366.1) From Silicibacter Sp. Tm1040 At
1.95 A Resolution
Length = 208
Score = 70.9 bits (172), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 77/165 (46%), Gaps = 20/165 (12%)
Query: 64 SLKVLCSQ--RREIPVVEARHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVK 121
+L LC R P R +V L+G PG+GKSTL+ + A++ +Q
Sbjct: 3 TLAALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPL-----------AAALSAQGL 51
Query: 122 PPDVATVLPMDGFHLYLSQLDAMEDPKEAHARRGAPWTFXXXXXXXXXXXXXXQGSVYAP 181
P A V+P DGFHL + + +P+ R+GAP TF Q V P
Sbjct: 52 P---AEVVPXDGFHLD----NRLLEPRGLLPRKGAPETFDFEGFQRLCHALKHQERVIYP 104
Query: 182 SFDHGVGDPVEDDILVGLQHKVVIVDGNYLFLDGGVWKDVSSMFD 226
FD + VG + +V I++GNYL D W+D+++++D
Sbjct: 105 LFDRARDIAIAGAAEVGPECRVAIIEGNYLLFDAPGWRDLTAIWD 149
>pdb|2GA8|A Chain A, Crystal Structure Of Yfh7 From Saccharomyces Cerevisiae: A
Putative P-Loop Containing Kinase With A Circular
Permutation.
pdb|2GAA|A Chain A, Crystal Structure Of Yfh7 From Saccharomyces Cerevisiae: A
Putative P-Loop Containing Kinase With A Circular
Permutation
Length = 359
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/127 (26%), Positives = 51/127 (40%), Gaps = 29/127 (22%)
Query: 124 DVATVLPMDGFHLYLSQLDAMEDPKEAHARRGAPWTFXXXXXXXXXXXXXXQG------- 176
++A ++PMDGFHL LD +DP+ AH RRG+P TF
Sbjct: 154 NIAQIVPMDGFHLSRRCLDLFKDPQTAHKRRGSPSTFDSNNFLQLCKILAKTSLXKVSSH 213
Query: 177 ----------------------SVYAPSFDHGVGDPVEDDILVGLQHKVVIVDGNYLFLD 214
++ P F+H + DP D + ++VI++G YL D
Sbjct: 214 HKFYSTSSVFEKLSKTFSQTIPDIFVPGFNHALKDPTPDQYCISKFTRIVILEGLYLLYD 273
Query: 215 GGVWKDV 221
WK +
Sbjct: 274 QENWKKI 280
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 81 RHIVGLAGPPGAGKSTLAAEVVRRINKIW 109
R V L G PG+GKST+A E+ + IN+ +
Sbjct: 24 RVCVILVGSPGSGKSTIAEELXQIINEKY 52
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 49 QPVFGKTR--SLVQNKTSLKVLCSQRREIPVVEARHI--VGLAGPPGAGKSTLAAEVVRR 104
QP+ + R +L Q +L + + +EA H+ + L GPPG GK+TL AEV+ R
Sbjct: 14 QPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTL-AEVIAR 72
Query: 105 INKIWPQKASSFDSQVK 121
++ S+ S VK
Sbjct: 73 YANADVERISAVTSGVK 89
>pdb|3TQC|A Chain A, Structure Of The Pantothenate Kinase (Coaa) From Coxiella
Burnetii
pdb|3TQC|B Chain B, Structure Of The Pantothenate Kinase (Coaa) From Coxiella
Burnetii
Length = 321
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 61/144 (42%), Gaps = 18/144 (12%)
Query: 82 HIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLPMDGFHLYLSQL 141
+I+G+AG GKST + V++ + WP P+V V+ DGF LY
Sbjct: 93 YIIGIAGSVAVGKST-TSRVLKALLSRWPDH----------PNVE-VITTDGF-LY---S 136
Query: 142 DAMEDPKEAHARRGAPWTFXX-XXXXXXXXXXXXQGSVYAPSFDHGVGDPVEDDILVGLQ 200
+A + + R+G P ++ Q +V P + H D V + Q
Sbjct: 137 NAKLEKQGLMKRKGFPESYDMPSLLRVLNAIKSGQRNVRIPVYSHHYYDIVRGQYEIVDQ 196
Query: 201 HKVVIVDGNYLFLDGGVWKDVSSM 224
+VI++G + L GV K + +
Sbjct: 197 PDIVILEGLNI-LQTGVRKTLQQL 219
>pdb|2WWW|A Chain A, Crystal Structure Of Methylmalonic Acidemia Type A
Protein
pdb|2WWW|B Chain B, Crystal Structure Of Methylmalonic Acidemia Type A
Protein
pdb|2WWW|C Chain C, Crystal Structure Of Methylmalonic Acidemia Type A
Protein
pdb|2WWW|D Chain D, Crystal Structure Of Methylmalonic Acidemia Type A
Protein
Length = 349
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 13/14 (92%)
Query: 84 VGLAGPPGAGKSTL 97
VGL+GPPGAGKST
Sbjct: 77 VGLSGPPGAGKSTF 90
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 83 IVGLAGPPGAGKSTLAAEVVRRINK 107
I+ LAGPPG GK++LA + + + +
Sbjct: 110 ILCLAGPPGVGKTSLAKSIAKSLGR 134
>pdb|1YQT|A Chain A, Rnase-L Inhibitor
Length = 538
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 75 IPVVEARHIVGLAGPPGAGKST 96
+PVV+ +VG+ GP G GKST
Sbjct: 41 LPVVKEGXVVGIVGPNGTGKST 62
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 70 SQRREIPVVEARHIVGLAGPPGAGKSTLAAEVVRRINKI 108
SQ + V R + + GPPG GK+ +A +V ++KI
Sbjct: 364 SQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKI 402
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 59 VQNKTSLKVLCSQRREIPVVEARHIVGLAGPPGAGKSTLA 98
V+ K SL + ++ R E V LAGPPG GK+TLA
Sbjct: 33 VKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLA 68
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 59 VQNKTSLKVLCSQRREIPVVEARHIVGLAGPPGAGKSTLA 98
V+ K SL + ++ R E V LAGPPG GK+TLA
Sbjct: 33 VKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLA 68
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 59 VQNKTSLKVLCSQRREIPVVEARHIVGLAGPPGAGKSTLA 98
V+ K SL + ++ R E V LAGPPG GK+TLA
Sbjct: 33 VKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLA 68
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 59 VQNKTSLKVLCSQRREIPVVEARHIVGLAGPPGAGKSTLA 98
V+ K SL + ++ R E V LAGPPG GK+TLA
Sbjct: 33 VKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLA 68
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 59 VQNKTSLKVLCSQRREIPVVEARHIVGLAGPPGAGKSTLA 98
V+ K SL + ++ R E V LAGPPG GK+TLA
Sbjct: 33 VKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLA 68
>pdb|2I3B|A Chain A, Solution Structure Of A Human Cancer-Related Nucleoside
Triphosphatase
Length = 189
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 20/27 (74%), Gaps = 4/27 (14%)
Query: 80 ARHIVGLAGPPGAGKSTL---AAEVVR 103
ARH+ L GPPG GK+TL A+EV++
Sbjct: 1 ARHVF-LTGPPGVGKTTLIHKASEVLK 26
>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
Length = 312
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 86 LAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLP---MDGFHLYLSQLD 142
L GPPG GK+TLA + + + +S + KP D+A +L +G L++ ++
Sbjct: 43 LFGPPGLGKTTLAHVIAHELG--VNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIH 100
Query: 143 AMEDPKEAH 151
+ E H
Sbjct: 101 RLSRQAEEH 109
>pdb|1KAG|A Chain A, Crystal Structure Of The Escherichia Coli Shikimate Kinase
I (Arok)
pdb|1KAG|B Chain B, Crystal Structure Of The Escherichia Coli Shikimate Kinase
I (Arok)
Length = 173
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 77 VVEARHIVGLAGPPGAGKSTLAAEVVRRIN 106
+ E R+I L GP GAGKST+ ++ +++N
Sbjct: 1 MAEKRNIF-LVGPMGAGKSTIGRQLAQQLN 29
>pdb|1UDX|A Chain A, Crystal Structure Of The Conserved Protein Tt1381 From
Thermus Thermophilus Hb8
Length = 416
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 84 VGLAGPPGAGKSTLAAEVVRRINKIWP 110
VGL G P AGKS+L A + R KI P
Sbjct: 160 VGLVGYPNAGKSSLLAAMTRAHPKIAP 186
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 86 LAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLP---MDGFHLYLSQLD 142
L GPPG GK+TLA + + + +S + KP D+A +L +G L++ ++
Sbjct: 43 LFGPPGLGKTTLAHVIAHELG--VNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIH 100
Query: 143 AMEDPKEAH 151
+ E H
Sbjct: 101 RLSRQAEEH 109
>pdb|4DBL|C Chain C, Crystal Structure Of E159q Mutant Of Btucdf
pdb|4DBL|D Chain D, Crystal Structure Of E159q Mutant Of Btucdf
pdb|4DBL|H Chain H, Crystal Structure Of E159q Mutant Of Btucdf
pdb|4DBL|I Chain I, Crystal Structure Of E159q Mutant Of Btucdf
Length = 249
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 78 VEARHIVGLAGPPGAGKSTLAAEV 101
V A I+ L GP GAGKSTL A +
Sbjct: 23 VRAGEILHLVGPNGAGKSTLLARM 46
>pdb|4FI3|C Chain C, Structure Of Vitamin B12 Transporter Btucd-F In A
Nucleotide-Bound State
pdb|4FI3|D Chain D, Structure Of Vitamin B12 Transporter Btucd-F In A
Nucleotide-Bound State
Length = 249
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 78 VEARHIVGLAGPPGAGKSTLAAEV 101
V A I+ L GP GAGKSTL A +
Sbjct: 23 VRAGEILHLVGPNGAGKSTLLARM 46
>pdb|2C9O|A Chain A, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|B Chain B, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|C Chain C, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
Length = 456
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 75 IPVVEARHIVG----LAGPPGAGKSTLAAEVVRRINKIWP 110
+ +++++ + G LAGPPG GK+ LA + + + P
Sbjct: 53 VELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVP 92
>pdb|1YE8|A Chain A, Crystal Structure Of Thep1 From The Hyperthermophile
Aquifex Aeolicus
Length = 178
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 86 LAGPPGAGKSTLAAEVVRRINK 107
+ G PG GK+TL ++V R+ K
Sbjct: 5 ITGEPGVGKTTLVKKIVERLGK 26
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 86 LAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLP---MDGFHLYLSQLD 142
L GPPG GK+TLA + + + +S + KP D+A +L +G L++ ++
Sbjct: 43 LFGPPGLGKTTLAHVIAHELGVNL--RVTSGPAIEKPGDLAAILANSLEEGDILFIDEIH 100
Query: 143 AMEDPKEAH 151
+ E H
Sbjct: 101 RLSRQAEEH 109
>pdb|3J15|B Chain B, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 593
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 75 IPVVEARHIVGLAGPPGAGKST 96
+P+V+ +VG+ GP G GK+T
Sbjct: 97 LPIVKDGMVVGIVGPNGTGKTT 118
>pdb|3BK7|A Chain A, Structure Of The Complete Abce1RNAASE-L Inhibitor Protein
From Pyrococcus Abysii
Length = 607
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 75 IPVVEARHIVGLAGPPGAGKST 96
+P+V+ +VG+ GP G GK+T
Sbjct: 111 LPIVKDGMVVGIVGPNGTGKTT 132
>pdb|2XSZ|A Chain A, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|B Chain B, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|C Chain C, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 367
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 84 VGLAGPPGAGKSTLAAEVVRRINKIWP 110
V LAGPPG GK+ LA + + + P
Sbjct: 80 VLLAGPPGTGKTALALAIAQELGSKVP 106
>pdb|2QI9|C Chain C, Abc-Transporter Btucd In Complex With Its Periplasmic
Binding Protein Btuf
pdb|2QI9|D Chain D, Abc-Transporter Btucd In Complex With Its Periplasmic
Binding Protein Btuf
Length = 249
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 78 VEARHIVGLAGPPGAGKSTLAA 99
V A I+ L GP GAGKSTL A
Sbjct: 23 VRAGEILHLVGPNGAGKSTLLA 44
>pdb|1L7V|C Chain C, Bacterial Abc Transporter Involved In B12 Uptake
pdb|1L7V|D Chain D, Bacterial Abc Transporter Involved In B12 Uptake
Length = 249
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 15/22 (68%)
Query: 78 VEARHIVGLAGPPGAGKSTLAA 99
V A I+ L GP GAGKSTL A
Sbjct: 23 VRAGEILHLVGPNGAGKSTLLA 44
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
0.317 0.133 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,868,651
Number of Sequences: 62578
Number of extensions: 258017
Number of successful extensions: 1027
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 976
Number of HSP's gapped (non-prelim): 68
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
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: 50 (23.9 bits)