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= psy16643
(165 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1H2S|A Chain A, Molecular Basis Of Transmenbrane Signalling By Sensory
Rhodopsin Ii-Transducer Complex
Length = 225
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 56/132 (42%), Gaps = 13/132 (9%)
Query: 38 VEEYSVLAKKVIQWLIIITLLIY-----AGFFCFE-----DLPTILLICGVLAQVLHLII 87
V E +V A + I W++ L++Y AG E L T++++ G ++
Sbjct: 63 VAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-- 120
Query: 88 IQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYFQSNYHSFAEVMAFFTLCLWLV-PFSLLV 146
I+ + + + AF+ V +V + S S S + T+ LW + PF L+
Sbjct: 121 IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLL 180
Query: 147 SLSANDMVLPTV 158
++ PTV
Sbjct: 181 GPPGVALLTPTV 192
>pdb|2F93|A Chain A, K Intermediate Structure Of Sensory Rhodopsin IiTRANSDUCER
COMPLEX IN Combination With The Ground State Structure
pdb|2F95|A Chain A, M Intermediate Structure Of Sensory Rhodopsin IiTRANSDUCER
COMPLEX IN Combination With The Ground State Structure
Length = 248
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 56/132 (42%), Gaps = 13/132 (9%)
Query: 38 VEEYSVLAKKVIQWLIIITLLIY-----AGFFCFE-----DLPTILLICGVLAQVLHLII 87
V E +V A + I W++ L++Y AG E L T++++ G ++
Sbjct: 62 VAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-- 119
Query: 88 IQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYFQSNYHSFAEVMAFFTLCLWLV-PFSLLV 146
I+ + + + AF+ V +V + S S S + T+ LW + PF L+
Sbjct: 120 IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLL 179
Query: 147 SLSANDMVLPTV 158
++ PTV
Sbjct: 180 GPPGVALLTPTV 191
>pdb|1GU8|A Chain A, Sensory Rhodopsin Ii
pdb|1GUE|A Chain A, Sensory Rhodopsin Ii
pdb|1H68|A Chain A, Sensory Rhodopsin Ii
pdb|3QAP|A Chain A, Crystal Structure Of Natronomonas Pharaonis Sensory
Rhodopsin Ii In The Ground State
pdb|3QDC|A Chain A, Crystal Structure Of Natronomonas Pharaonis Sensory
Rhodopsin Ii In The Active State
Length = 239
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 56/132 (42%), Gaps = 13/132 (9%)
Query: 38 VEEYSVLAKKVIQWLIIITLLIY-----AGFFCFE-----DLPTILLICGVLAQVLHLII 87
V E +V A + I W++ L++Y AG E L T++++ G ++
Sbjct: 63 VAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-- 120
Query: 88 IQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYFQSNYHSFAEVMAFFTLCLWLV-PFSLLV 146
I+ + + + AF+ V +V + S S S + T+ LW + PF L+
Sbjct: 121 IERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLL 180
Query: 147 SLSANDMVLPTV 158
++ PTV
Sbjct: 181 GPPGVALLTPTV 192
>pdb|2KSY|A Chain A, Solution Nmr Structure Of Sensory Rhodopsin Ii
Length = 247
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 55/132 (41%), Gaps = 13/132 (9%)
Query: 38 VEEYSVLAKKVIQWLIIITLLIY-----AGFFCFE-----DLPTILLICGVLAQVLHLII 87
V E +V + I W++ L++Y AG E L T++++ G ++
Sbjct: 63 VAERTVFVPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-- 120
Query: 88 IQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYFQSNYHSFAEVMAFFTLCLWLV-PFSLLV 146
I+ + + + AFI V +V + S S S + T+ LW + PF L+
Sbjct: 121 IERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLL 180
Query: 147 SLSANDMVLPTV 158
++ PTV
Sbjct: 181 GPPGVALLTPTV 192
>pdb|1JGJ|A Chain A, Crystal Structure Of Sensory Rhodopsin Ii At 2.4
Angstroms: Insights Into Color Tuning And Transducer
Interaction
Length = 217
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 31/132 (23%), Positives = 55/132 (41%), Gaps = 13/132 (9%)
Query: 38 VEEYSVLAKKVIQWLIIITLLIY-----AGFFCFE-----DLPTILLICGVLAQVLHLII 87
V E +V + I W++ L++Y AG E L T++++ G ++
Sbjct: 63 VAERTVFVPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPG-- 120
Query: 88 IQNFPYVSLTSPAFIAAVVLIVVNHYYAMSYFQSNYHSFAEVMAFFTLCLWLV-PFSLLV 146
I+ + + + AFI V +V + S S S + T+ LW + PF L+
Sbjct: 121 IERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLL 180
Query: 147 SLSANDMVLPTV 158
++ PTV
Sbjct: 181 GPPGVALLTPTV 192
>pdb|2WW9|A Chain A, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|A Chain A, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
Length = 490
Score = 26.2 bits (56), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 48 VIQWLIIITLLIYAGFFCFEDLPTI--------LLICGVLAQVLHLIIIQNFPYVSLTSP 99
++Q++I+ + I+AG+F +DL + L+ G+ +L +I + F + +S
Sbjct: 125 IVQYVILTNIFIFAGYFG-DDLSVVQIGLINFQLVGAGIFTTLLAEVIDKGFGF---SSG 180
Query: 100 AFIAAVVLIVVN 111
A I V+I N
Sbjct: 181 AMIINTVVIATN 192
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
0.331 0.143 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,392,557
Number of Sequences: 62578
Number of extensions: 148105
Number of successful extensions: 295
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 12
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 bits)