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= 025293
(255 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 = 68.6 bits (166), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 45/146 (30%), Positives = 71/146 (48%), Gaps = 18/146 (12%)
Query: 107 KHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLPMDGFHLYLSQ 166
+ +V L+G PG+GKSTL+ + A++ +Q P A V+P DGFHL
Sbjct: 22 RQLVALSGAPGSGKSTLSNPL-----------AAALSAQGLP---AEVVPXDGFHLD--- 64
Query: 167 LDAMEDPKEAHARRGAPWTFXXXXXXXXXXXXXXQGSVYAPSFDHGVGDPVEDDILVGLQ 226
+ + +P+ R+GAP TF Q V P FD + VG +
Sbjct: 65 -NRLLEPRGLLPRKGAPETFDFEGFQRLCHALKHQERVIYPLFDRARDIAIAGAAEVGPE 123
Query: 227 HKVVIVDGNYLFLDGGVWKDVSSMFD 252
+V I++GNYL D W+D+++++D
Sbjct: 124 CRVAIIEGNYLLFDAPGWRDLTAIWD 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: 150 DVATVLPMDGFHLYLSQLDAMEDPKEAHARRGAPWTFXXXXXXXXXXXXXXQG------- 202
++A ++PMDGFHL LD +DP+ AH RRG+P TF
Sbjct: 154 NIAQIVPMDGFHLSRRCLDLFKDPQTAHKRRGSPSTFDSNNFLQLCKILAKTSLXKVSSH 213
Query: 203 ----------------------SVYAPSFDHGVGDPVEDDILVGLQHKVVIVDGNYLFLD 240
++ P F+H + DP D + ++VI++G YL D
Sbjct: 214 HKFYSTSSVFEKLSKTFSQTIPDIFVPGFNHALKDPTPDQYCISKFTRIVILEGLYLLYD 273
Query: 241 GGVWKDV 247
WK +
Sbjct: 274 QENWKKI 280
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 105 NVKHIVGLAGPPGAGKSTLAAEVVRRINKIW 135
N + V L G PG+GKST+A E+ + IN+ +
Sbjct: 22 NYRVCVILVGSPGSGKSTIAEELXQIINEKY 52
>pdb|3NDB|B Chain B, Crystal Structure Of A Signal Sequence Bound To The Signal
Recognition Particle
Length = 454
Score = 33.9 bits (76), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 21/95 (22%)
Query: 56 RSLVQNKTSLKVLCSQRREIPVVEARCMDE---------------VYDALAQRLLPTSAL 100
R+L+Q ++K++ +EI E R ++E VY+ L +LL A
Sbjct: 35 RALIQADVNVKLVLKMSKEI---ERRALEEKTPKGLSKKEHIIKIVYEELV-KLLGEEAK 90
Query: 101 ASNVNVK--HIVGLAGPPGAGKSTLAAEVVRRINK 133
+N K +++ L G G+GK+T AA++ R I K
Sbjct: 91 KLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQK 125
>pdb|2V3C|C Chain C, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
pdb|2V3C|D Chain D, Crystal Structure Of The Srp54-Srp19-7s.S Srp Rna Complex
Of M. Jannaschii
Length = 432
Score = 33.9 bits (76), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 21/95 (22%)
Query: 56 RSLVQNKTSLKVLCSQRREIPVVEARCMDE---------------VYDALAQRLLPTSAL 100
R+L+Q ++K++ +EI E R ++E VY+ L +LL A
Sbjct: 35 RALIQADVNVKLVLKMSKEI---ERRALEEKTPKGLSKKEHIIKIVYEELV-KLLGEEAK 90
Query: 101 ASNVNVK--HIVGLAGPPGAGKSTLAAEVVRRINK 133
+N K +++ L G G+GK+T AA++ R I K
Sbjct: 91 KLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQK 125
>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 = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 47/192 (24%), Positives = 77/192 (40%), Gaps = 33/192 (17%)
Query: 74 EIPVVEARCMDEVYDALAQRLLPTSALASNV--------------NVKHIVGLAGPPGAG 119
+I +V + + E+Y L+ RLL A V +I+G+AG G
Sbjct: 46 QIEIVSLKEVTEIYLPLS-RLLSFYVTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVG 104
Query: 120 KSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKEAHAR 179
KST + V++ + WP P+V V+ DGF LY +A + + R
Sbjct: 105 KST-TSRVLKALLSRWPDH----------PNVE-VITTDGF-LY---SNAKLEKQGLMKR 148
Query: 180 RGAPWTFXX-XXXXXXXXXXXXQGSVYAPSFDHGVGDPVEDDILVGLQHKVVIVDGNYLF 238
+G P ++ Q +V P + H D V + Q +VI++G +
Sbjct: 149 KGFPESYDMPSLLRVLNAIKSGQRNVRIPVYSHHYYDIVRGQYEIVDQPDIVILEGLNI- 207
Query: 239 LDGGVWKDVSSM 250
L GV K + +
Sbjct: 208 LQTGVRKTLQQL 219
>pdb|1W5S|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5S|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
pdb|1W5T|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
pdb|1W5T|C Chain C, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
Complexes)
Length = 412
Score = 30.8 bits (68), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
EA + +Y RLL + L S+VN+ I G G G GK+TLA V+R+++ ++
Sbjct: 30 EAEALARIY---LNRLLSGAGL-SDVNM--IYGSIGRVGIGKTTLAKFTVKRVSEAAAKE 83
Query: 139 A----SSFDSQVKPPDVATVLPM 157
++ + P++ T+L +
Sbjct: 84 GLTVKQAYVNAFNAPNLYTILSL 106
>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 = 0.92, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 20/82 (24%)
Query: 84 DEVYDALAQRLLPTSALASNVNVKHIVG------------------LAGPPGAGKSTLAA 125
D + LA R+ P + LA + +H++ L GPPG GK+TL A
Sbjct: 10 DNTFQPLAARMRPEN-LAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTL-A 67
Query: 126 EVVRRINKIWPQKASSFDSQVK 147
EV+ R ++ S+ S VK
Sbjct: 68 EVIARYANADVERISAVTSGVK 89
>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 = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 13/14 (92%)
Query: 110 VGLAGPPGAGKSTL 123
VGL+GPPGAGKST
Sbjct: 77 VGLSGPPGAGKSTF 90
>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
Length = 312
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 93 RLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVA 152
R+ +A A ++H++ L GPPG GK+TLA + + + +S + KP D+A
Sbjct: 25 RVYLEAAKARKEPLEHLL-LFGPPGLGKTTLAHVIAHELG--VNLRVTSGPAIEKPGDLA 81
Query: 153 TVLP---MDGFHLYLSQLDAMEDPKEAH 177
+L +G L++ ++ + E H
Sbjct: 82 AILANSLEEGDILFIDEIHRLSRQAEEH 109
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 93 RLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVA 152
R+ +A A ++H++ L GPPG GK+TLA + + + +S + KP D+A
Sbjct: 25 RVYLEAAKARKEPLEHLL-LFGPPGLGKTTLAHVIAHELGVNL--RVTSGPAIEKPGDLA 81
Query: 153 TVLP---MDGFHLYLSQLDAMEDPKEAH 177
+L +G L++ ++ + E H
Sbjct: 82 AILANSLEEGDILFIDEIHRLSRQAEEH 109
>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 = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 98 SALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQVKPPDVATVLP- 156
+A A ++H++ L GPPG GK+TLA + + + +S + KP D+A +L
Sbjct: 30 AAKARKEPLEHLL-LFGPPGLGKTTLAHVIAHELGVNL--RVTSGPAIEKPGDLAAILAN 86
Query: 157 --MDGFHLYLSQLDAMEDPKEAH 177
+G L++ ++ + E H
Sbjct: 87 SLEEGDILFIDEIHRLSRQAEEH 109
>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 = 2.3, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 109 IVGLAGPPGAGKSTLAAEVVRRINK 133
I+ LAGPPG GK++LA + + + +
Sbjct: 110 ILCLAGPPGVGKTSLAKSIAKSLGR 134
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 81 RCMDEVY--DALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVR 129
R +DEV D + QRL N+ H++ +GPPG GK+ A + R
Sbjct: 14 RTLDEVVGQDEVIQRL---KGYVERKNIPHLL-FSGPPGTGKTATAIALAR 60
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 81 RCMDEVY--DALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVR 129
R +DEV D + QRL N+ H++ +GPPG GK+ A + R
Sbjct: 14 RTLDEVVGQDEVIQRL---KGYVERKNIPHLL-FSGPPGTGKTATAIALAR 60
>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 = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 100 LASNVNVKHIVGLAGPPGAGKSTLAAEV 127
L+ V I+ L GP GAGKSTL A +
Sbjct: 19 LSGEVRAGEILHLVGPNGAGKSTLLARM 46
>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 = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 100 LASNVNVKHIVGLAGPPGAGKSTLAAEV 127
L+ V I+ L GP GAGKSTL A +
Sbjct: 19 LSGEVRAGEILHLVGPNGAGKSTLLARM 46
>pdb|1UDX|A Chain A, Crystal Structure Of The Conserved Protein Tt1381 From
Thermus Thermophilus Hb8
Length = 416
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 110 VGLAGPPGAGKSTLAAEVVRRINKIWP 136
VGL G P AGKS+L A + R KI P
Sbjct: 160 VGLVGYPNAGKSSLLAAMTRAHPKIAP 186
>pdb|1YE8|A Chain A, Crystal Structure Of Thep1 From The Hyperthermophile
Aquifex Aeolicus
Length = 178
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 112 LAGPPGAGKSTLAAEVVRRINK 133
+ G PG GK+TL ++V R+ K
Sbjct: 5 ITGEPGVGKTTLVKKIVERLGK 26
>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 = 6.6, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 110 VGLAGPPGAGKSTLAAEVVRRINKIWP 136
V LAGPPG GK+ LA + + + P
Sbjct: 66 VLLAGPPGTGKTALALAIAQELGSKVP 92
>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 = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 100 LASNVNVKHIVGLAGPPGAGKSTLAA 125
L+ V I+ L GP GAGKSTL A
Sbjct: 19 LSGEVRAGEILHLVGPNGAGKSTLLA 44
>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 = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 100 LASNVNVKHIVGLAGPPGAGKSTLAA 125
L+ V I+ L GP GAGKSTL A
Sbjct: 19 LSGEVRAGEILHLVGPNGAGKSTLLA 44
>pdb|1MV5|A Chain A, Crystal Structure Of Lmra Atp-Binding Domain
pdb|1MV5|B Chain B, Crystal Structure Of Lmra Atp-Binding Domain
pdb|1MV5|C Chain C, Crystal Structure Of Lmra Atp-Binding Domain
pdb|1MV5|D Chain D, Crystal Structure Of Lmra Atp-Binding Domain
Length = 243
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 77 VVEARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTL 123
++ AR +D YD Q L S A I+ AGP G GKST+
Sbjct: 1 MLSARHVDFAYDDSEQILRDISFEA---QPNSIIAFAGPSGGGKSTI 44
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 112 LAGPPGAGKSTLAAEVVRRINKI 134
+ GPPG GK+ +A +V ++KI
Sbjct: 380 IQGPPGTGKTVTSATIVYHLSKI 402
>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 = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 107 KHIVGLAGPPGAGKSTLAAEVVRRIN 132
K + L GP GAGKST+ ++ +++N
Sbjct: 4 KRNIFLVGPMGAGKSTIGRQLAQQLN 29
>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 = 8.0, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 112 LAGPPGAGKSTLAAEVVRRINKIWP 136
LAGPPG GK+ LA + + + P
Sbjct: 82 LAGPPGTGKTALALAIAQELGSKVP 106
>pdb|3CMV|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|B Chain B, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|C Chain C, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|E Chain E, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|F Chain F, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|G Chain G, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMV|H Chain H, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 1357
Score = 27.3 bits (59), Expect = 8.5, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 6 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 65
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 66 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 112
Score = 27.3 bits (59), Expect = 8.5, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 355 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 414
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 415 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 461
Score = 27.3 bits (59), Expect = 8.5, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 704 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 763
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 764 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 810
Score = 27.3 bits (59), Expect = 8.5, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1054 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1113
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1114 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1160
>pdb|3CMU|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 2050
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 6 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 65
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 66 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 112
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 355 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 414
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 415 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 461
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 704 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 763
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 764 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 810
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1053 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1112
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1113 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1159
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1399 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1458
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1459 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1505
Score = 27.3 bits (59), Expect = 9.1, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1747 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1806
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1807 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1853
>pdb|3CMT|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMT|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMW|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMW|C Chain C, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMX|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
pdb|3CMX|D Chain D, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 1706
Score = 27.3 bits (59), Expect = 9.2, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 6 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 65
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 66 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 112
Score = 27.3 bits (59), Expect = 9.2, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 355 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 414
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 415 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 461
Score = 27.3 bits (59), Expect = 9.2, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 704 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 763
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 764 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 810
Score = 27.3 bits (59), Expect = 9.2, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1054 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1113
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1114 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1160
Score = 27.3 bits (59), Expect = 9.2, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 3/107 (2%)
Query: 79 EARCMDEVYDALAQRLLPTSALASNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQK 138
E R MD + L + A + + IV + GP +GK+TL +V+ +
Sbjct: 1403 EDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTC 1462
Query: 139 ASSFDSQVKPPDVATVLPMDGFHLYLSQLDAMEDPKE---AHARRGA 182
A P A L +D +L SQ D E E A AR GA
Sbjct: 1463 AFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA 1509
>pdb|2ZM5|A Chain A, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
pdb|2ZM5|B Chain B, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
Length = 316
Score = 27.3 bits (59), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 102 SNVNVKHIVGLAGPPGAGKSTLAAEVVRRINKIWPQKASSFDSQV--KPPDVATVLP 156
S ++ + L GP +GK+ LA E + KI P + S DS + K D+ T P
Sbjct: 5 SKASLPKAIFLXGPTASGKTALAIE----LRKILPVELISVDSALIYKGXDIGTAKP 57
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,474,471
Number of Sequences: 62578
Number of extensions: 279414
Number of successful extensions: 999
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 967
Number of HSP's gapped (non-prelim): 50
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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)