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= psy14644
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OE0|A Chain A, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Cyclic Peptide Antagonist Cvx15
pdb|3OE9|A Chain A, Crystal Structure Of The Chemokine Cxcr4 Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE9|B Chain B, Crystal Structure Of The Chemokine Cxcr4 Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
Length = 499
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 55 NIYVEVSKRKGINFCGTNRALRGNIIDNSNVKLATV--LDSTPGGTIRL-------RMND 105
N+ ++ + F + R L+ D + V LA + TP R+ +
Sbjct: 338 NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDA 397
Query: 106 VSNINKTRIRTLKMTVIIVLTFFWCWTPYVI 136
S + + LK TVI++L FF CW PY I
Sbjct: 398 YSGSGHQKRKALKPTVILILAFFACWLPYYI 428
>pdb|3OE6|A Chain A, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In I222
Spacegroup
Length = 508
Score = 33.9 bits (76), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 115 RTLKMTVIIVLTFFWCWTPYVI 136
+ LK TVI++L FF CW PY I
Sbjct: 410 KALKTTVILILAFFACWLPYYI 431
>pdb|3ODU|A Chain A, The 2.5 A Structure Of The Cxcr4 Chemokine Receptor In
Complex With Small Molecule Antagonist It1t
pdb|3ODU|B Chain B, The 2.5 A Structure Of The Cxcr4 Chemokine Receptor In
Complex With Small Molecule Antagonist It1t
pdb|3OE8|A Chain A, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE8|B Chain B, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
pdb|3OE8|C Chain C, Crystal Structure Of The Cxcr4 Chemokine Receptor In
Complex With A Small Molecule Antagonist It1t In P1
Spacegroup
Length = 502
Score = 33.9 bits (76), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 115 RTLKMTVIIVLTFFWCWTPYVI 136
+ LK TVI++L FF CW PY I
Sbjct: 410 KALKTTVILILAFFACWLPYYI 431
>pdb|2Z73|A Chain A, Crystal Structure Of Squid Rhodopsin
pdb|2Z73|B Chain B, Crystal Structure Of Squid Rhodopsin
pdb|3AYM|A Chain A, Crystal Structure Of The Batho Intermediate Of Squid
Rhodopsin
pdb|3AYM|B Chain B, Crystal Structure Of The Batho Intermediate Of Squid
Rhodopsin
pdb|3AYN|A Chain A, Crystal Structure Of Squid Isorhodopsin
pdb|3AYN|B Chain B, Crystal Structure Of Squid Isorhodopsin
Length = 448
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 25/120 (20%), Positives = 47/120 (39%), Gaps = 24/120 (20%)
Query: 20 SFNSFASDTHERYYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFCGTNRALRGNI 79
SF+ + D+ R ++ + P+ II F YFNI + VS
Sbjct: 187 SFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVS------------------ 228
Query: 80 IDNSNVKLATVLDSTPGGTIRLRMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYVIMTV 139
N ++A + +R + +R K++++IV F W+PY ++ +
Sbjct: 229 --NHEKEMAAMAKRLNAKELRKAQAGAN----AEMRLAKISIVIVSQFLLSWSPYAVVAL 282
>pdb|2ZIY|A Chain A, Crystal Structure Of Squid Rhodopsin
Length = 372
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/120 (20%), Positives = 47/120 (39%), Gaps = 24/120 (20%)
Query: 20 SFNSFASDTHERYYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFCGTNRALRGNI 79
SF+ + D+ R ++ + P+ II F YFNI + VS
Sbjct: 186 SFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVS------------------ 227
Query: 80 IDNSNVKLATVLDSTPGGTIRLRMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYVIMTV 139
N ++A + +R + +R K++++IV F W+PY ++ +
Sbjct: 228 --NHEKEMAAMAKRLNAKELRKAQAGAN----AEMRLAKISIVIVSQFLLSWSPYAVVAL 281
>pdb|3OAX|A Chain A, Crystal Structure Of Bovine Rhodopsin With Beta-Ionone
pdb|3OAX|B Chain B, Crystal Structure Of Bovine Rhodopsin With Beta-Ionone
pdb|1GZM|A Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form
pdb|1GZM|B Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form
pdb|1HZX|A Chain A, Crystal Structure Of Bovine Rhodopsin
pdb|1HZX|B Chain B, Crystal Structure Of Bovine Rhodopsin
pdb|2I36|A Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I36|B Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I36|C Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State
Rhodopsin
pdb|2I35|A Chain A, Crystal Structure Of Rhombohedral Crystal Form Of
Ground-State Rhodopsin
pdb|2I37|A Chain A, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2I37|B Chain B, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2I37|C Chain C, Crystal Structure Of A Photoactivated Rhodopsin
pdb|2HPY|A Chain A, Crystallographic Model Of Lumirhodopsin
pdb|2HPY|B Chain B, Crystallographic Model Of Lumirhodopsin
pdb|2PED|A Chain A, Crystallographic Model Of 9-Cis-Rhodopsin
pdb|2PED|B Chain B, Crystallographic Model Of 9-Cis-Rhodopsin
pdb|2G87|A Chain A, Crystallographic Model Of Bathorhodopsin
pdb|2G87|B Chain B, Crystallographic Model Of Bathorhodopsin
pdb|1L9H|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms
Resolution
pdb|1L9H|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms
Resolution
pdb|1U19|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms
Resolution
pdb|1U19|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms
Resolution
Length = 349
Score = 28.9 bits (63), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I+V+ F CW PY
Sbjct: 237 QQQESATTQKAEKEVTRMVIIMVIAFLICWLPYA 270
>pdb|1JFP|A Chain A, Structure Of Bovine Rhodopsin (Dark Adapted)
pdb|1LN6|A Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii)
pdb|3CAP|A Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled
Receptor Rhodopsin In Its Ligand-Free State
pdb|3CAP|B Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled
Receptor Rhodopsin In Its Ligand-Free State
pdb|3C9L|A Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal
Crystal Form
pdb|1F88|A Chain A, Crystal Structure Of Bovine Rhodopsin
pdb|1F88|B Chain B, Crystal Structure Of Bovine Rhodopsin
pdb|3DQB|A Chain A, Crystal Structure Of The Active G-protein-coupled Receptor
Opsin In Complex With A C-terminal Peptide Derived From
The Galpha Subunit Of Transducin
pdb|3PQR|A Chain A, Crystal Structure Of Metarhodopsin Ii In Complex With A
C-Terminal Peptide Derived From The Galpha Subunit Of
Transducin
pdb|3PXO|A Chain A, Crystal Structure Of Metarhodopsin Ii
Length = 348
Score = 28.9 bits (63), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I+V+ F CW PY
Sbjct: 236 QQQESATTQKAEKEVTRMVIIMVIAFLICWLPYA 269
>pdb|2J4Y|A Chain A, Crystal Structure Of A Rhodopsin Stabilizing Mutant
Expressed In Mammalian Cells
pdb|2J4Y|B Chain B, Crystal Structure Of A Rhodopsin Stabilizing Mutant
Expressed In Mammalian Cells
Length = 349
Score = 28.9 bits (63), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I+V+ F CW PY
Sbjct: 237 QQQESATTQKAEKEVTRMVIIMVIAFLICWLPYA 270
>pdb|3C9M|A Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal
Crystal Form
Length = 348
Score = 28.9 bits (63), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I+V+ F CW PY
Sbjct: 236 QQQESATTQKAEKEVTRMVIIMVIAFLICWLPYA 269
>pdb|2X72|A Chain A, Crystal Structure Of The Constitutively Active E113q,N2c,
D282c Rhodopsin Mutant With Bound Galphact Peptide
Length = 349
Score = 28.9 bits (63), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I+V+ F CW PY
Sbjct: 237 QQQESATTQKAEKEVTRMVIIMVIAFLICWLPYA 270
>pdb|4A4M|A Chain A, Crystal Structure Of The Light-Activated Constitutively
Active N2c,M257y,D282c Rhodopsin Mutant In Complex With
A Peptide Resembling The C-Terminus Of The
Galpha-Protein Subunit (Gact)
Length = 349
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 102 RMNDVSNINKTRIRTLKMTVIIVLTFFWCWTPYV 135
+ + + K +M +I V+ F CW PY
Sbjct: 237 QQQESATTQKAEKEVTRMVIIYVIAFLICWLPYA 270
>pdb|1UH2|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-AmylaseMALTO-Hexaose
Complex
pdb|1UH4|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1MALTO-
Tridecaose Complex
pdb|2D0G|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 1 (Tvai) Mutant D356nE396Q COMPLEXED WITH
P5, A Pullulan Model Oligosaccharide
pdb|2D0H|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 1 (Tvai) Mutant D356nE396Q COMPLEXED WITH
P2, A Pullulan Model Oligosaccharide
Length = 637
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 12 HPNFTQCVSFNSFASDTHER--YYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFC 69
HP F + +F+S + + +YNY+T Y P F FN + +N+
Sbjct: 272 HPWFDKYNNFSSQGAYESQSSPWYNYYT---FYTWPDSYASFLGFNSLPK------LNYG 322
Query: 70 GTNRALRGNIIDNSNVKLATVLD 92
+ A+RG I +NSN T L+
Sbjct: 323 NSGSAVRGVIYNNSNSVAKTYLN 345
>pdb|2D0F|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
Alpha- Amylase 1 (Tvai) Mutant D356n Complexed With P2,
A Pullulan Model Oligosaccharide
Length = 637
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 12 HPNFTQCVSFNSFASDTHER--YYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFC 69
HP F + +F+S + + +YNY+T Y P F FN + +N+
Sbjct: 272 HPWFDKYNNFSSQGAYESQSSPWYNYYT---FYTWPDSYASFLGFNSLPK------LNYG 322
Query: 70 GTNRALRGNIIDNSNVKLATVLD 92
+ A+RG I +NSN T L+
Sbjct: 323 NSGSAVRGVIYNNSNSVAKTYLN 345
>pdb|1JI1|A Chain A, Crystal Structure Analysis Of Thermoactinomyces Vulgaris
R- 47 Alpha-amylase 1
pdb|1JI1|B Chain B, Crystal Structure Analysis Of Thermoactinomyces Vulgaris
R- 47 Alpha-amylase 1
pdb|1UH3|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-AmylaseACARBOSE
Complex
Length = 637
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 12 HPNFTQCVSFNSFASDTHER--YYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFC 69
HP F + +F+S + + +YNY+T Y P F FN + +N+
Sbjct: 272 HPWFDKYNNFSSQGAYESQSSPWYNYYT---FYTWPDSYASFLGFNSLPK------LNYG 322
Query: 70 GTNRALRGNIIDNSNVKLATVLD 92
+ A+RG I +NSN T L+
Sbjct: 323 NSGSAVRGVIYNNSNSVAKTYLN 345
>pdb|1IZK|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-amylase 1 Mutant
Enzyme W398v
Length = 637
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 12 HPNFTQCVSFNSFASDTHER--YYNYFTVVVMYVIPMCIIVFSYFNIYVEVSKRKGINFC 69
HP F + +F+S + + +YNY+T Y P F FN + +N+
Sbjct: 272 HPWFDKYNNFSSQGAYESQSSPWYNYYT---FYTWPDSYASFLGFNSLPK------LNYG 322
Query: 70 GTNRALRGNIIDNSNVKLATVLD 92
+ A+RG I +NSN T L+
Sbjct: 323 NSGSAVRGVIYNNSNSVAKTYLN 345
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
0.329 0.141 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,959,744
Number of Sequences: 62578
Number of extensions: 142056
Number of successful extensions: 336
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 314
Number of HSP's gapped (non-prelim): 25
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 46 (22.3 bits)