RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780817|ref|YP_003065230.1| preprotein translocase subunit
SecB [Candidatus Liberibacter asiaticus str. psy62]
(152 letters)
>gnl|CDD|145603 pfam02556, SecB, Preprotein translocase subunit SecB. This family
consists of preprotein translocase subunit SecB. SecB is
required for the normal export of envelope proteins out
of the cell cytoplasm.
Length = 147
Score = 163 bits (416), Expect = 1e-41
Identities = 54/136 (39%), Positives = 87/136 (63%), Gaps = 2/136 (1%)
Query: 5 QKQAFTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDI 64
+ F I QY+KD SFE+PNAP F ++ QP + + + VNA ++ ++V+L+ +
Sbjct: 9 PQPQFQIQRQYVKDLSFENPNAPAIF--LEEWQPEVNVQLNVNARKLAENVYEVVLTVTV 66
Query: 65 EAKNNDKVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGGFP 124
AKN +K F +E+ +GI I + P+E + L +ECP +LFP+ R+IIS+ R GGFP
Sbjct: 67 TAKNEEKTAFLVEVKQAGIFTIRNVPEEQLHPFLGIECPNILFPYAREIISDLTRRGGFP 126
Query: 125 PLVIDTIDFLKLFQQE 140
PL++ I+F L++Q+
Sbjct: 127 PLMLAPINFDALYEQQ 142
>gnl|CDD|32135 COG1952, SecB, Preprotein translocase subunit SecB [Intracellular
trafficking and secretion].
Length = 157
Score = 149 bits (378), Expect = 3e-37
Identities = 54/147 (36%), Positives = 90/147 (61%), Gaps = 2/147 (1%)
Query: 3 KKQKQAFTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSF 62
+ +F I Y+KD SFE+PNAPH F ++ QP + +++ NAN ++ F+V+L+
Sbjct: 7 PTGQPSFNIQRIYVKDLSFEAPNAPHIF--QKDWQPEVNLDLNTNANQLAENVFEVVLTV 64
Query: 63 DIEAKNNDKVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGG 122
+ AK +K F E+ +GI RI P+E ++ +L +ECP +LFP+ R++IS+ GG
Sbjct: 65 TVTAKLGEKTAFLCEVQQAGIFRIAGIPEEQMAHLLGIECPNILFPYARELISDLTARGG 124
Query: 123 FPPLVIDTIDFLKLFQQEKSLIKNKEG 149
FPPL++ I+F L+ Q + + +E
Sbjct: 125 FPPLMLAPINFDALYAQRLAEQQAEEV 151
>gnl|CDD|29643 cd00557, Translocase_SecB, Preprotein translocase subunit SecB.
SecB is a cytoplasmic component of the multisubunit
membrane-bound enzyme termed Sec protein translocase,
which is the main constituent of the General Secretory
(type II) Pathway involved in translocation of nascent
polypeptides across the cytoplasmic membrane. SecB has
been shown to function as export-specific molecular
chaperone that selectively binds preproteins, maintains
them in a translocation competent state and delivers
them to SecA, the membrane-bound ATPase, that drives the
translocation reaction. In solution, SecB exists as
homotetramer, which is organized as a dimer of dimers..
Length = 131
Score = 92.3 bits (229), Expect = 5e-20
Identities = 40/131 (30%), Positives = 70/131 (53%), Gaps = 4/131 (3%)
Query: 9 FTILNQYIKDFSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGAD-FDVILSFDIEAK 67
I Y+KD SFE+PNAPH F ++ +P + +++ + + ++V+L+ AK
Sbjct: 1 LQIQRIYVKDISFEAPNAPHLF--QKDWKPRLNLDLDTEITQLKNDNKYEVVLNITAGAK 58
Query: 68 NND-KVIFRLELAYSGILRILDCPQEHISQILFVECPQLLFPFVRQIISNTIRDGGFPPL 126
K F E+ +G+ I+ + ++ L + CP +LFP+ R++IS+ FPPL
Sbjct: 59 LEFAKSAFYCEVKQAGVFEIIGIEIDQMAHCLEINCPAILFPYARELISSITARATFPPL 118
Query: 127 VIDTIDFLKLF 137
+ I+F LF
Sbjct: 119 NLPPINFDALF 129
>gnl|CDD|34525 COG4916, COG4916, Uncharacterized protein containing a TIR
(Toll-Interleukin 1-resistance) domain [Function
unknown].
Length = 329
Score = 26.9 bits (59), Expect = 2.6
Identities = 10/50 (20%), Positives = 16/50 (32%)
Query: 19 FSFESPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDIEAKN 68
+ + F + I+ V S D +SF EA+N
Sbjct: 141 RTVPDASLRRDLFTFETILLREPIHATVTVVDSSEKPVDSGISFAGEARN 190
>gnl|CDD|144627 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of
this family are implicated in bringing cargo forward
from the ER and binding to coat proteins by their
cytoplasmic domains. This domain corresponds closely to
the beta-strand rich GOLD domain described in. The GOLD
domain is always found combined with lipid- or
membrane-association domains.
Length = 177
Score = 26.5 bits (59), Expect = 3.4
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 18 DFSFE-SPNAPHCFFDIQNQQPTIKINVQVNANTISGADFDVILSFDIEAKN-NDKVIFR 75
+FE CF++ + + + QV ISG D+ F + + N VI+
Sbjct: 1 ALTFELPAGEKECFYEEVPKGTLVTGSYQV----ISGGGLDI--DFTVTDPDGNGNVIYS 54
Query: 76 LELAYSG 82
+ G
Sbjct: 55 KKRKSEG 61
>gnl|CDD|145140 pfam01819, Levi_coat, Levivirus coat protein. The Levivirus coat
protein forms the bacteriophage coat that encapsidates
the viral RNA. 180 copies of this protein form the
virion shell. The MS2 bacteriophage coat protein
controls two distinct processes: sequence-specific RNA
encapsidation and repression of replicase translation-by
binding to an RNA stem-loop structure of 19 nucleotides
containing the initiation codon of the replicase gene.
The binding of a coat protein dimer to this hairpin
shuts off synthesis of the viral replicase, switching
the viral replication cycle to virion assembly rather
than continued replication.
Length = 129
Score = 25.2 bits (55), Expect = 6.9
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 34 QNQQPTIKINVQ-VNANTISGADF---------DVILSFDIEAKNNDKVIFRLELA 79
++ TIK+ V V T++G + DV L+ I + ++ R ELA
Sbjct: 55 NRRKYTIKLEVPKVTTQTVNGVELPVVARTSYADVDLTIPIFSTTKERAFIRKELA 110
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.325 0.142 0.411
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,836,298
Number of extensions: 92004
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 15
Length of query: 152
Length of database: 6,263,737
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,426,972
Effective search space: 296607124
Effective search space used: 296607124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)