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= 008601
(560 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4EV6|A Chain A, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|B Chain B, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|C Chain C, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|D Chain D, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
pdb|4EV6|E Chain E, The Complete Structure Of Cora Magnesium Transporter From
Methanocaldococcus Jannaschii
Length = 339
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 420 TIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTV---ITGLFGINVDGIPGADNTPY 476
T ++V+ S + L ++++ + + + V ITG++G+N +P A+N P
Sbjct: 255 TYREVLTSMMDITLSLENIKMNQIMKILTMVTTIFAVPMWITGIYGMNFSYLPLANN-PQ 313
Query: 477 AFGLFTAILFFIGVVLIAV 495
F L A++ I ++ + +
Sbjct: 314 GFWLVMALMVVIIMIFVYI 332
>pdb|3BO0|A Chain A, Ribosome-Secy Complex
pdb|3BO1|A Chain A, Ribosome-Secy Complex
pdb|3KCR|A Chain A, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
Length = 442
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 75 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 129
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 130 -AFGILTPLLAFLVIIQIAFGSIILIYL 156
>pdb|2BBJ|A Chain A, Crystal Structure Of The Cora Mg2+ Transporter
pdb|2BBJ|B Chain B, Crystal Structure Of The Cora Mg2+ Transporter
pdb|2BBJ|D Chain D, Crystal Structure Of The Cora Mg2+ Transporter
pdb|2BBJ|E Chain E, Crystal Structure Of The Cora Mg2+ Transporter
pdb|2BBJ|F Chain F, Crystal Structure Of The Cora Mg2+ Transporter
pdb|2HN2|A Chain A, Crystal Structure Of The Cora Mg2+ Transporter Homologue
From T. Maritima In Complex With Divalent Cations
pdb|2HN2|B Chain B, Crystal Structure Of The Cora Mg2+ Transporter Homologue
From T. Maritima In Complex With Divalent Cations
pdb|2HN2|C Chain C, Crystal Structure Of The Cora Mg2+ Transporter Homologue
From T. Maritima In Complex With Divalent Cations
pdb|2HN2|D Chain D, Crystal Structure Of The Cora Mg2+ Transporter Homologue
From T. Maritima In Complex With Divalent Cations
pdb|2HN2|E Chain E, Crystal Structure Of The Cora Mg2+ Transporter Homologue
From T. Maritima In Complex With Divalent Cations
Length = 354
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/140 (17%), Positives = 63/140 (45%), Gaps = 8/140 (5%)
Query: 358 QEIRRLSRQVIRVKWSLHAREEIVFELYQHLRGNVARTLLEGIRKNAREMIEEQEAVRGR 417
Q +L R ++ ++ ++ E++ LY+ + + + + R I+ + V
Sbjct: 212 QRTHQLKRNLVELRKTIWPLREVLSSLYRDVPPLIEKETVPYFRDVYDHTIQIADTVE-- 269
Query: 418 LFTIQDVMQSTVRAWLQ---DRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNT 474
T +D++ + +L +++ V L + + LT I G++G+N + +P
Sbjct: 270 --TFRDIVSGLLDVYLSSVSNKTNEVMKVLTIIATIFMPLTFIAGIYGMNFEYMPEL-RW 326
Query: 475 PYAFGLFTAILFFIGVVLIA 494
+ + + A++ I V+++
Sbjct: 327 KWGYPVVLAVMGVIAVIMVV 346
>pdb|2IUB|A Chain A, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|B Chain B, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|C Chain C, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|D Chain D, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|E Chain E, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|F Chain F, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|G Chain G, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|H Chain H, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|I Chain I, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution.
pdb|2IUB|J Chain J, Crystal Structure Of A Divalent Metal Ion Transporter Cora
At 2.9 A Resolution
Length = 363
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/140 (17%), Positives = 63/140 (45%), Gaps = 8/140 (5%)
Query: 358 QEIRRLSRQVIRVKWSLHAREEIVFELYQHLRGNVARTLLEGIRKNAREMIEEQEAVRGR 417
Q +L R ++ ++ ++ E++ LY+ + + + + R I+ + V
Sbjct: 221 QRTHQLKRNLVELRKTIWPLREVLSSLYRDVPPLIEKETVPYFRDVYDHTIQIADTVE-- 278
Query: 418 LFTIQDVMQSTVRAWLQ---DRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNT 474
T +D++ + +L +++ V L + + LT I G++G+N + +P
Sbjct: 279 --TFRDIVSGLLDVYLSSVSNKTNEVMKVLTIIATIFMPLTFIAGIYGMNFEYMPEL-RW 335
Query: 475 PYAFGLFTAILFFIGVVLIA 494
+ + + A++ I V+++
Sbjct: 336 KWGYPVVLAVMGVIAVIMVV 355
>pdb|1RH5|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 76 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 130
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 131 -AFGILTPLLAFLVIIQIAFGSIILIYL 157
>pdb|1RHZ|A Chain A, The Structure Of A Protein Conducting Channel
Length = 436
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 76 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 130
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 131 -AFGILTPLLAFLVIIQIAFGSIILIYL 157
>pdb|2YXQ|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 431
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 71 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 125
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 126 -AFGILTPLLAFLVIIQIAFGSIILIYL 152
>pdb|2YXR|A Chain A, The Plug Domain Of The Secy Protein Stablizes The Closed
State Of The Translocation Channel And Maintains A
Membrane Seal
Length = 426
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 66 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 120
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 121 -AFGILTPLLAFLVIIQIAFGSIILIYL 147
>pdb|3DKN|A Chain A, Sec61 In The Canine Ribosome-Channel Complex From The
Endoplasmic Reticulum
Length = 430
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 416 GRLFTIQDVMQSTVRAWLQDRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNTP 475
G + T +MQ V + + L + N A+F GC +L++I + GA
Sbjct: 75 GPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCF--VEAVLFVGAG--- 129
Query: 476 YAFGLFTAILFFIGVVLIAVG---LLYL 500
AFG+ T +L F+ ++ IA G L+YL
Sbjct: 130 -AFGILTPLLAFLVIIQIAFGSIILIYL 156
>pdb|4EEB|A Chain A, Cora Coiled-Coil Mutant Under Mg2+ Absence
pdb|4EEB|B Chain B, Cora Coiled-Coil Mutant Under Mg2+ Absence
pdb|4EEB|C Chain C, Cora Coiled-Coil Mutant Under Mg2+ Absence
pdb|4EEB|D Chain D, Cora Coiled-Coil Mutant Under Mg2+ Absence
pdb|4EEB|E Chain E, Cora Coiled-Coil Mutant Under Mg2+ Absence
pdb|4EED|A Chain A, Cora Coiled-Coil Mutant Under Mg2+ Presence
pdb|4EED|B Chain B, Cora Coiled-Coil Mutant Under Mg2+ Presence
pdb|4EED|C Chain C, Cora Coiled-Coil Mutant Under Mg2+ Presence
pdb|4EED|D Chain D, Cora Coiled-Coil Mutant Under Mg2+ Presence
pdb|4EED|E Chain E, Cora Coiled-Coil Mutant Under Mg2+ Presence
Length = 330
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 24/140 (17%), Positives = 62/140 (44%), Gaps = 8/140 (5%)
Query: 358 QEIRRLSRQVIRVKWSLHAREEIVFELYQHLRGNVARTLLEGIRKNAREMIEEQEAVRGR 417
Q +L R ++ + ++ E++ LY+ + + + + R I+ + V
Sbjct: 188 QRTHQLKRNLVELAATIWPLREVLSSLYRDVPPLIEKETVPYFRDVYDHTIQIADTVE-- 245
Query: 418 LFTIQDVMQSTVRAWLQ---DRSLRVTHNLAVFGGCGVVLTVITGLFGINVDGIPGADNT 474
T +D++ + +L +++ V L + + LT I G++G+N + +P
Sbjct: 246 --TFRDIVSGLLDVYLSSVSNKTNEVMKVLTIIATIFMPLTFIAGIYGMNFEYMPEL-RW 302
Query: 475 PYAFGLFTAILFFIGVVLIA 494
+ + + A++ I V+++
Sbjct: 303 KWGYPVVLAVMGVIAVIMVV 322
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
0.320 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,942,555
Number of Sequences: 62578
Number of extensions: 636780
Number of successful extensions: 1308
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 1306
Number of HSP's gapped (non-prelim): 25
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)