RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1135
(124 letters)
>gnl|CDD|222976 PHA03087, PHA03087, G protein-coupled chemokine receptor-like
protein; Provisional.
Length = 335
Score = 36.3 bits (84), Expect = 0.002
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 40 IILYGVTILSGVALNIFAIYHIIVERLFRDATCGYFINIALADIIKCMFVLPITLMVTLV 99
I++Y G+ NI IY ++ + + Y +N+A++D++ M LP + ++
Sbjct: 44 IVVYSTIFFFGLVGNIIVIY-VLTKTKIKTPMDIYLLNLAVSDLLFVM-TLPFQIYYYIL 101
Query: 100 QNWTWGSFLCYFLPMLQLIPF 120
W++G F C + L I F
Sbjct: 102 FQWSFGEFACKIVSGLYYIGF 122
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 28.8 bits (65), Expect = 0.83
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 60 HIIVERLFRDATCGYFINIALADIIKCMFVLPITLMVTLVQNWTWGSFLCYFLPMLQLIP 119
+ +E + +A GYF L ++ + V L Q+W G L P LIP
Sbjct: 105 TLALEGV--EALDGYFARY-LPQLVLAVIVPLAILAAVFPQDWISGLILLLTAP---LIP 158
Query: 120 F 120
Sbjct: 159 I 159
>gnl|CDD|215646 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).
This family contains, amongst other G-protein-coupled
receptors (GCPRs), members of the opsin family, which
have been considered to be typical members of the
rhodopsin superfamily. They share several motifs, mainly
the seven transmembrane helices, GCPRs of the rhodopsin
superfamily. All opsins bind a chromophore, such as
11-cis-retinal. The function of most opsins other than
the photoisomerases is split into two steps: light
absorption and G-protein activation. Photoisomerases, on
the other hand, are not coupled to G-proteins - they are
thought to generate and supply the chromophore that is
used by visual opsins.
Length = 251
Score = 26.9 bits (60), Expect = 2.9
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 74 YFINIALADIIKCMFVLPITLMVTLVQNWTWGSFLC 109
+ +N+A+AD++ + + P L + +W +G LC
Sbjct: 16 FLLNLAVADLLFLLTLPPWALYYLVGGDWPFGDALC 51
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 26.3 bits (58), Expect = 6.0
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 77 NIALADIIKCMFVLPITLMVTLVQ 100
NI ++DIIK + +L +MVT+ Q
Sbjct: 22 NIKVSDIIKKLMLL--GVMVTINQ 43
>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
Length = 323
Score = 25.6 bits (56), Expect = 8.0
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 34 NVYVFFIILYGVTILSGVALNIFAIYHIIVERLFRDATCGYFINIALADIIKCMFVLPIT 93
+V F I+ Y + + G+ N+ I +IV+R F Y NIA++D++ +F P
Sbjct: 26 DVNYFVIVFYILLFIFGLIGNVLVIAVLIVKR-FMFVVDVYLFNIAMSDLM-LVFSFPFI 83
Query: 94 LMVTLVQNWTWGSFLC 109
+ L W +G F+C
Sbjct: 84 IHNDL-NEWIFGEFMC 98
>gnl|CDD|236068 PRK07630, PRK07630, CobD/CbiB family protein; Provisional.
Length = 312
Score = 25.4 bits (56), Expect = 8.7
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 30 PTLLNVYVFFIILYGVTILSGVALNIFAIYHIIVERLFRDATCGYFINIALA 81
P +L V + + +LY V+ + N+ +Y + R F YF +I LA
Sbjct: 57 PWVLAVALVYYLLYKVSPVLAFLWNVAVLYLTLGFRQFSH----YFTDIHLA 104
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.335 0.148 0.478
Gapped
Lambda K H
0.267 0.0842 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,512,205
Number of extensions: 594392
Number of successful extensions: 1150
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1140
Number of HSP's successfully gapped: 90
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 53 (24.0 bits)