RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5734
(205 letters)
>gnl|CDD|216181 pfam00902, TatC, Sec-independent protein translocase protein
(TatC). The bacterial Tat system has a remarkable
ability to transport folded proteins even enzyme
complexes across the cytoplasmic membrane. It is
structurally and mechanistically similar to the Delta
pH-driven thylakoidal protein import pathway. A
functional Tat system or Delta pH-dependent pathway
requires three integral membrane proteins: TatA/Tha4,
TatB/Hcf106 and TatC/cpTatC. The TatC protein is
essential for the function of both pathways. It might be
involved in twin-arginine signal peptide recognition,
protein translocation and proton translocation. Sequence
analysis predicts that TatC contains six transmembrane
helices (TMHs), and experimental data confirmed that N-
and C-termini of TatC or cpTatC are exposed to the
cytoplasmic or stromal face of the membrane. The
cytoplasmic N-terminus and the first cytoplasmic loop
region of the Escherichia coli TatC protein are
essential for protein export. At least two TatC
molecules co-exist within each Tat translocon.
Length = 212
Score = 29.0 bits (66), Expect = 1.5
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 11 REKLLFYTTAFFILLAIFSLFGFLFLVPFVIE 42
R LL + A F+L + + F + ++P ++
Sbjct: 95 RRFLLPFVFASFLLFLLGAAFAYFVVLPIALK 126
>gnl|CDD|237481 PRK13723, PRK13723, conjugal transfer pilus assembly protein TraH;
Provisional.
Length = 451
Score = 28.6 bits (64), Expect = 2.6
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 80 EGCTREIYECTQITVSYKVSVNTSVQSTITAQSLRLYNRFRRAVLG-----EDDVLLPSF 134
EG T +IY C KV +T+V TI+ + L ++ + + D L
Sbjct: 271 EGGTAKIYHCNDSDKCLKVVADTNV--TIS-RDNALKSQITKLLTSIQNKAVSDTPLTDK 327
Query: 135 EDNFLETPAIP 145
E F+ + IP
Sbjct: 328 EKGFISSTTIP 338
>gnl|CDD|213575 TIGR00964, secE_bact, preprotein translocase, SecE subunit,
bacterial. This model represents exclusively the
bacterial (and some organellar) SecE protein. SecE is
part of the core heterotrimer, SecYEG, of the Sec
preprotein translocase system. Other components are the
ATPase SecA, a cytosolic chaperone SecB, and an
accessory complex of SecDF and YajC [Protein fate,
Protein and peptide secretion and trafficking].
Length = 55
Score = 26.0 bits (58), Expect = 2.9
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 10 SREKLLFYTTAFFILLAIFSLFGFLFLVPFVI 41
SR++L+ YT + + FSL FLFLV +V
Sbjct: 19 SRKELITYTIVVIVFVIFFSL--FLFLVDYVF 48
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 28.7 bits (64), Expect = 3.0
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 83 TREIYECTQITVSYKVSVNTSVQSTITAQSLRLYNRFRRAVLGEDDVLLPSFEDNFLE 140
T++I E T + Y+ V V+ TI + + FRRA+ +D+ +L + +F+E
Sbjct: 591 TKKILEPTHGIIVYQEQVINLVK-TIANFDIATADNFRRAISKKDEKILIQLKKDFIE 647
>gnl|CDD|218031 pfam04335, VirB8, VirB8 protein. VirB8 is a bacterial virulence
protein with cytoplasmic, transmembrane, and
periplasmic regions. It is thought that it is a primary
constituent of a DNA transporter. The periplasmic
region interacts with VirB9, VirB10, and itself. This
family also includes the conjugal transfer protein
family TrbF, a family of proteins known to be involved
in conjugal transfer. The TrbF protein is thought to
compose part of the pilus required for transfer. This
domain has a similar fold to the NTF2 protein.
Length = 208
Score = 28.0 bits (63), Expect = 3.1
Identities = 8/47 (17%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 2 AEEAGKESSREKLLFYTTAFFILLAIFSLFGFLFL------VPFVIE 42
+ G + + + + LA+ ++ L VP+V+E
Sbjct: 7 DDRIGSARVQRRRWWLVAFGSLALAVLAVGAVAVLAPLKTVVPYVVE 53
>gnl|CDD|217431 pfam03219, TLC, TLC ATP/ADP transporter.
Length = 491
Score = 28.0 bits (63), Expect = 3.9
Identities = 10/26 (38%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 10 SREKLLFYTTAFFILLAIFSLFGFLF 35
SREK+ + +FF++ F+LF F+
Sbjct: 87 SREKVFYIIISFFLVF--FALFAFVL 110
>gnl|CDD|223004 PHA03173, PHA03173, UL37 tegument protein; Provisional.
Length = 1028
Score = 28.1 bits (63), Expect = 4.3
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 55 VPATCETIQVENLRGASNCSWTSCREGCTREIYECTQITVSYKVSVNTSVQSTITAQSLR 114
VPA + AS + E R+ +E Q + S + +++ T Q R
Sbjct: 334 VPAVLRLLSSGEPDDASAAAKARVAE-HARQTWEAIQASTSPSQVIEALIEAGFTRQHCR 392
Query: 115 LYNRFRRAVLG 125
L RA+
Sbjct: 393 LL---ERALED 400
>gnl|CDD|222726 pfam14387, DUF4418, Domain of unknown function (DUF4418). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
archaea. Proteins in this family are typically between
132 and 150 amino acids in length.
Length = 123
Score = 26.8 bits (60), Expect = 4.6
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 23 ILLAIFSLFGFLFLVPFVIEPACTTIMREFDEVPATC 59
L I L L L PFV+ P C+ M D P C
Sbjct: 1 ALQLILGLL--LALAPFVLAPVCSPHM--ADGGPMKC 33
>gnl|CDD|201325 pfam00584, SecE, SecE/Sec61-gamma subunits of protein
translocation complex. SecE is part of the SecYEG
complex in bacteria which translocates proteins from
the cytoplasm. In eukaryotes the complex, made from
Sec61-gamma and Sec61-alpha translocates protein from
the cytoplasm to the ER. Archaea have a similar
complex.
Length = 56
Score = 25.6 bits (57), Expect = 4.8
Identities = 6/26 (23%), Positives = 14/26 (53%)
Query: 10 SREKLLFYTTAFFILLAIFSLFGFLF 35
+R++ L T + + + +LF +L
Sbjct: 20 TRKETLKTTVVVLVFVLVMALFLWLV 45
>gnl|CDD|227812 COG5525, COG5525, Phage terminase, large subunit GpA [Replication,
recombination and repair].
Length = 611
Score = 27.4 bits (61), Expect = 6.1
Identities = 11/41 (26%), Positives = 15/41 (36%)
Query: 113 LRLYNRFRRAVLGEDDVLLPSFEDNFLETPAIPEGNSSEWD 153
+YNR G + P D F + A +G WD
Sbjct: 508 EMIYNRLGADEPGPGYIHFPDDPDIFDQLTAEQKGLDGRWD 548
>gnl|CDD|220342 pfam09685, Tic20, Tic20-like protein. Chloroplast function
requires the import of nuclear encoded proteins from
the cytoplasm across the chloroplast double membrane.
This is accomplished by two protein complexes, the Toc
complex located at the outer membrane and the Tic
complex located at the inner membrane. The Toc complex
recognises specific proteins by a cleavable N-terminal
sequence and is primarily responsible for translocation
through the outer membrane, while the Tic complex
translocates the protein through the inner membrane.
This entry represents Tic20, a core member of the Tic
complex. This protein is deeply embedded in the inner
envelope membrane and is thought to function as a
protein- conducting component of the Tic complex. This
family also includes many proteins of unknown function
from non-synthetic organisms.
Length = 104
Score = 26.3 bits (59), Expect = 6.2
Identities = 14/36 (38%), Positives = 16/36 (44%)
Query: 14 LLFYTTAFFILLAIFSLFGFLFLVPFVIEPACTTIM 49
LL YT IL I GFL L+ I TI+
Sbjct: 49 LLIYTVILGILSFILGFIGFLLLILLWILSLVFTII 84
>gnl|CDD|236066 PRK07597, secE, preprotein translocase subunit SecE; Reviewed.
Length = 64
Score = 24.9 bits (55), Expect = 8.6
Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 10 SREKLLFYTTAFFILLAIFSLFGFLFLVPFVI 41
+R++L+ T + +A F+L F +LV +
Sbjct: 28 TRKELVRSTIVVLVFVAFFAL--FFYLVDLLF 57
>gnl|CDD|150442 pfam09771, Tmemb_18A, Transmembrane protein 188. The function of
this family of transmembrane proteins has not, as yet,
been determined.
Length = 126
Score = 25.9 bits (57), Expect = 9.3
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 9 SSREKLLFYTTAFFILLAIFSLFGF--LFLVPFVIEPACTTIMREFD 53
S +T + LL +F +FG + P +I C T++ EF+
Sbjct: 61 DSLWNHPDFTFSTLTLLLLF-VFGIHKRVVAPSIIASRCRTVLAEFN 106
>gnl|CDD|221975 pfam13197, DUF4013, Protein of unknown function (DUF4013). This is
a family of uncharacterized proteins that is found in
archaea and bacteria.
Length = 167
Score = 26.1 bits (58), Expect = 10.0
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 10 SREKLLFYTTAFFILLAIFSLFGFLFLVPFVI 41
SR L Y AF +++ I + G L + I
Sbjct: 136 SRIGWLAYLLAFLVVIVIGLVVGLLGALIVGI 167
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
0.323 0.138 0.427
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,327,672
Number of extensions: 926191
Number of successful extensions: 1584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1578
Number of HSP's successfully gapped: 49
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.7 bits)