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= 036637
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C1Y|A Chain A, Structure Of Bacterial Dna Damage Sensor Protein With Co-
Purified And Co-Crystallized Ligand
pdb|3C1Y|B Chain B, Structure Of Bacterial Dna Damage Sensor Protein With Co-
Purified And Co-Crystallized Ligand
pdb|3C1Z|A Chain A, Structure Of The Ligand-Free Form Of A Bacterial Dna
Damage Sensor Protein
pdb|3C1Z|B Chain B, Structure Of The Ligand-Free Form Of A Bacterial Dna
Damage Sensor Protein
pdb|3C21|A Chain A, Structure Of A Bacterial Dna Damage Sensor Protein With
Reaction Product
pdb|3C21|B Chain B, Structure Of A Bacterial Dna Damage Sensor Protein With
Reaction Product
pdb|3C23|A Chain A, Structure Of A Bacterial Dna Damage Sensor Protein With
Non- Reactive Ligand
pdb|3C23|B Chain B, Structure Of A Bacterial Dna Damage Sensor Protein With
Non- Reactive Ligand
Length = 377
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 122 IVELGEAGRFDRLSYRKALEDI---RLISNKDYEAFESRSSTLNNVLR 166
IVELGE GR R+ R+ ED+ ++ DY + E T N+L+
Sbjct: 230 IVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQ 277
>pdb|3QUW|A Chain A, Crystal Structure Of Yeast Mmf1
Length = 153
Score = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 177 GIYGMGGIGKTTLAKEVAIQFGRDQFFDQVIFV--EVPHIPDIRKIQGEIADKLGLIF 232
GI + + T LA A + + + ++V ++P+ PD + +QG I++K +F
Sbjct: 25 GITTLTPVS-TKLAPPAAASYSQAMKANNFVYVSGQIPYTPDNKPVQGSISEKAEQVF 81
>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 = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/32 (56%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 161 LNNVLRALQDPDVNMV-GIYGMGGIGKTTLAK 191
LN +L DVNM+ G G GIGKTTLAK
Sbjct: 39 LNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAK 70
>pdb|1F48|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1IHU|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase In Complex With
Mg-Adp-Alf3
pdb|1II0|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II0|B Chain B, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II9|A Chain A, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
pdb|1II9|B Chain B, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
Length = 589
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 175 MVGIYGMGGIGKTTLAKEVAIQFGRDQFFD 204
++ + G GG+GKTT+A +A++ D FD
Sbjct: 329 LIMLMGKGGVGKTTMAAAIAVRLA-DMGFD 357
>pdb|2YNM|A Chain A, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
pdb|2YNM|B Chain B, Structure Of The Adpxalf3-stabilized Transition State Of
The Nitrogenase-like Dark-operative Protochlorophyllide
Oxidoreductase Complex From Prochlorococcus Marinus With
Its Substrate Protochlorophyllide A
Length = 301
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 170 DPDVNM------VGIYGMGGIGKTTLAKEVAIQFGR 199
DP VN+ + +YG GGIGK+T + ++ F +
Sbjct: 25 DPKVNIEEGALVIAVYGKGGIGKSTTSSNLSAAFSK 60
>pdb|1SGW|A Chain A, Putative Abc Transporter (Atp-Binding Protein) From
Pyrococcus Furiosus Pfu-867808-001
Length = 214
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 174 NMVGIYGMGGIGKTTLAKEVAIQFGRDQFFDQVIFVEVPHIPDIRKIQGEI 224
N+V +G GIGKTTL K ++ ++I+ VP I K++G+I
Sbjct: 36 NVVNFHGPNGIGKTTLLKTISTYL--KPLKGEIIYNGVP----ITKVKGKI 80
>pdb|4HYZ|A Chain A, Crystal Structure Of A Hypothetical Protein (Rumgna_01855)
From Ruminococcus Gnavus Atcc 29149 At 2.25 A Resolution
pdb|4HYZ|B Chain B, Crystal Structure Of A Hypothetical Protein (Rumgna_01855)
From Ruminococcus Gnavus Atcc 29149 At 2.25 A Resolution
Length = 114
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 131 FDRLSYRK-ALEDIRLISNKDYEAFESR 157
FD+ + RK A EDI + +KDYE+++SR
Sbjct: 11 FDKETVRKQAXEDIEIAQSKDYESWKSR 38
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 28.1 bits (61), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 176 VGIYGMGGIGKTTLAKEVAIQFGRDQFF 203
V +YG G GKT LAK VA G + F
Sbjct: 218 VLLYGPPGTGKTLLAKAVAATIGANFIF 245
>pdb|3CMU|A Chain A, Mechanism Of Homologous Recombination From The Reca-
SsdnaDSDNA STRUCTURES
Length = 2050
Score = 27.3 bits (59), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 44/161 (27%), Positives = 64/161 (39%), Gaps = 13/161 (8%)
Query: 61 KGEEI---EKNVEKWLASVNNIITEAEKFTGDADKANKRCFMGLCPNLKTRHRFSKEAVR 117
KGE+I + N WL E EK + +N G + R E
Sbjct: 1316 KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSTTGATGAMSGRMSAIDE--N 1373
Query: 118 QQKAIVE-LGEAGR-FDRLSYRKALEDIRLISNKDYEAFESRSSTLNNVLRALQDPDVNM 175
+QKA+ LG+ + F + S + ED + D E + S +L+ L A P +
Sbjct: 1374 KQKALAAALGQIEKQFGKGSIMRLGEDRSM----DVETISTGSLSLDIALGAGGLPMGRI 1429
Query: 176 VGIYGMGGIGKTTLAKEVAIQFGRDQFFDQVIFVEVPHIPD 216
V IYG GKTTL +V R+ F++ H D
Sbjct: 1430 VEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALD 1468
>pdb|3PPN|A Chain A, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPN|B Chain B, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPO|A Chain A, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPO|B Chain B, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPP|A Chain A, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPP|B Chain B, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPQ|A Chain A, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPQ|B Chain B, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPR|A Chain A, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
pdb|3PPR|B Chain B, Structures Of The Substrate-Binding Protein Provide
Insights Into The Multiple Compatible Solutes Binding
Specificities Of Bacillus Subtilis Abc Transporter Opuc
Length = 311
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 1 MVESIVTVVLEVAKCLGRPTERQLSFVRNYRSNFENLKTELEKLKDDGASMQHGVDEGRR 60
M ES + + +A+ + T+ + V+N SN+ + L D A+ G D
Sbjct: 49 MTESEIVANM-IAQLIEHDTDLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTST 107
Query: 61 KGEEIEKNVEKWLASVNN 78
G+E EK+ +K L V N
Sbjct: 108 LGKEAEKDPKKALNIVQN 125
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
0.318 0.136 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,994,131
Number of Sequences: 62578
Number of extensions: 285643
Number of successful extensions: 1130
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1097
Number of HSP's gapped (non-prelim): 49
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
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)