RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5960
(121 letters)
>gnl|CDD|215908 pfam00413, Peptidase_M10, Matrixin. The members of this family are
enzymes that cleave peptides. These proteases require
zinc for catalysis.
Length = 159
Score = 111 bits (280), Expect = 1e-32
Identities = 49/92 (53%), Positives = 58/92 (63%), Gaps = 5/92 (5%)
Query: 19 RDELRRALDVWSKHSKLTFREVNDDRADILIYFEKENHWDGYPFDGPGKILAHAFFPGSG 78
R +RRA VWS+ + LTF EV ADI I F + H DGYPFDGPG +LAHAFFPG
Sbjct: 24 RRAIRRAFKVWSEVTPLTFTEVPTGTADIKIGFGRGEHGDGYPFDGPGGVLAHAFFPG-P 82
Query: 79 RGGDAHFDIDEDWMVLGVSRSANADEGKSLEL 110
GGD HFD DE W V +++ EG +L L
Sbjct: 83 IGGDIHFDDDEQWTV----GNSSGPEGTNLFL 110
>gnl|CDD|239805 cd04278, ZnMc_MMP, Zinc-dependent metalloprotease, matrix
metalloproteinase (MMP) sub-family. MMPs are
responsible for a great deal of pericellular
proteolysis of extracellular matrix and cell surface
molecules, playing crucial roles in morphogenesis, cell
fate specification, cell migration, tissue repair,
tumorigenesis, gain or loss of tissue-specific
functions, and apoptosis. In many instances, they are
anchored to cell membranes via trans-membrane domains,
and their activity is controlled via TIMPs (tissue
inhibitors of metalloproteinases).
Length = 157
Score = 109 bits (276), Expect = 5e-32
Identities = 47/79 (59%), Positives = 52/79 (65%), Gaps = 2/79 (2%)
Query: 14 DRGRLRDELRRALDVWSKHSKLTFREVNDDR-ADILIYFEKENHWDGYPFDGPGKILAHA 72
R +R + RA VWS + LTFREV + ADI I F + NH DGYPFDGPG LAHA
Sbjct: 19 PRDDVRRAIARAFRVWSDVTPLTFREVTSGQEADIRISFARGNHGDGYPFDGPGGTLAHA 78
Query: 73 FFPGSGRGGDAHFDIDEDW 91
FFPG G GGD HFD DE W
Sbjct: 79 FFPG-GIGGDIHFDDDEQW 96
>gnl|CDD|214576 smart00235, ZnMc, Zinc-dependent metalloprotease. Neutral zinc
metallopeptidases. This alignment represents a subset
of known subfamilies. Highest similarity occurs in the
HExxH zinc-binding site/ active site.
Length = 139
Score = 50.8 bits (122), Expect = 3e-09
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 15/75 (20%)
Query: 19 RDELRRALDVWSKHSKLTFREVNDDRADILIYFEKENHWDGYPFDGPGKILAHAFFPGSG 78
R+ + +AL WS + + F E ADI I F + G L+HA P
Sbjct: 24 REAIAKALAEWSDVTCIRFVERTGT-ADIYISFGSGDS---------GCTLSHAGRP--- 70
Query: 79 RGGDAHFDIDEDWMV 93
GGD H + + +
Sbjct: 71 -GGDQHLSL-GNGCI 83
>gnl|CDD|239804 cd04277, ZnMc_serralysin_like, Zinc-dependent metalloprotease,
serralysin_like subfamily. Serralysins and related
proteases are important virulence factors in pathogenic
bacteria. They may be secreted into the medium via a
mechanism found in gram-negative bacteria, that does not
require n-terminal signal sequences which are cleaved
after the transmembrane translocation. A calcium-binding
domain c-terminal to the metalloprotease domain, which
contains multiple tandem repeats of a nine-residue motif
including the pattern GGxGxD, and which forms a parallel
beta roll may be involved in the translocation mechanism
and/or substrate binding. Serralysin family members may
have a broad spectrum of substrates each, including host
immunoglobulins, complement proteins, cell matrix and
cytoskeletal proteins, as well as antimicrobial
peptides.
Length = 186
Score = 38.6 bits (90), Expect = 2e-04
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 23 RRALDVWSKHSKLTFREVND-DRADILIYFEKENHWDGYPFDGPGKILAHAFFPGSG--- 78
R AL+ W + + F EV+D ADI + + +A++PGSG
Sbjct: 40 RDALEAWEDVADIDFVEVSDNSGADIRFGNSSDPDGNTA---------GYAYYPGSGSGT 90
Query: 79 -RGGDAHFDIDEDW 91
GGD F+ D
Sbjct: 91 AYGGDIWFNSSYDT 104
>gnl|CDD|239819 cd04327, ZnMc_MMP_like_3, Zinc-dependent metalloprotease;
MMP_like sub-family 3. A group of bacterial and fungal
metalloproteinase domains similar to matrix
metalloproteinases and astacin.
Length = 198
Score = 35.0 bits (81), Expect = 0.004
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 18 LRDELRRALDVWSKHSKLTFREVNDDRADILIYFE 52
L+D++R A W ++ L F+ V D ADI I F
Sbjct: 21 LKDKVRAAAREWLPYANLKFKFVTDADADIRISFT 55
>gnl|CDD|224366 COG1449, COG1449, Alpha-amylase/alpha-mannosidase [Carbohydrate
transport and metabolism].
Length = 615
Score = 31.3 bits (71), Expect = 0.11
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 54 ENHWDGYPFDGPGKILAHAFFPGSGRGGDAHFDIDEDWM 92
E+ W+ Y +G + A + GD +++
Sbjct: 351 EHPWEFYETNGFEFL--RALPQELEKRGDIETVTPSEFI 387
>gnl|CDD|239493 cd03399, Band_7_flotillin, Band_7_flotillin: a subgroup of the
band 7 domain of flotillin (reggie) like proteins. This
subgroup contains proteins similar to stomatin,
prohibitin, flotillin, HlfK/C and podicin. These two
proteins are lipid raft-associated. Individual
proteins of this band 7 domain family may cluster to
form membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units
with their own regulatory functions. Flotillins have
been implicated in signal transduction, vesicle
trafficking, cytoskeleton rearrangement and, interact
with a variety of proteins. Flotillins may play a role
in the progression of prion disease, in the
pathogenesis of neurodegenerative diseases such as
Parkinson's and Alzheimer's disease and, in cancer
invasion and metastasis.
Length = 128
Score = 26.4 bits (59), Expect = 2.6
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 6/46 (13%)
Query: 1 MTLKHHPKRVRHYDRGRLRDELRRALDVWSKHSKLTFREVNDDRAD 46
L + + + L LR + +T E+ +DR
Sbjct: 47 RFLGKSEEEIEELVKEVLEGHLRAVV------GTMTVEEIYEDRDK 86
>gnl|CDD|220515 pfam10003, DUF2244, Integral membrane protein (DUF2244). This
domain, found in various bacterial hypothetical and
putative membrane proteins, has no known function.
Length = 140
Score = 26.3 bits (59), Expect = 2.7
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 1 MTLKHHPKRVR------HYDRGRLRDELRRAL 26
+TL+ + V +R L +ELRRAL
Sbjct: 109 LTLRSRGREVEIGRFLSPDEREALAEELRRAL 140
>gnl|CDD|237276 PRK13024, PRK13024, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 755
Score = 26.7 bits (60), Expect = 3.3
Identities = 20/80 (25%), Positives = 27/80 (33%), Gaps = 12/80 (15%)
Query: 16 GRLRDEL------RRALDVWSKHSKLTFREVNDDRADILIYFEKENHWDGYPFDGPGKIL 69
R+R EL RA ++ +KLTFR+V D + G +L
Sbjct: 88 NRIRVELPGVQDPERARELLGSTAKLTFRDVTDP-PPPGVGGPV----VGPDEGKDTAVL 142
Query: 70 AHAFFPGSG-RGGDAHFDID 88
G A FD D
Sbjct: 143 NPVLLSGDDLTDAGAKFDQD 162
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 26.8 bits (60), Expect = 3.3
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 93 VLGVSRSANADEGKS 107
+LGVS+ A+ +E K
Sbjct: 5 ILGVSKDASEEEIKK 19
>gnl|CDD|179169 PRK00924, PRK00924, 5-keto-4-deoxyuronate isomerase; Provisional.
Length = 276
Score = 26.3 bits (59), Expect = 4.3
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 5 HHPKRVRHYDRGRLRDE 21
HP+ + D LR+E
Sbjct: 7 IHPEDAKTLDTEGLREE 23
>gnl|CDD|236772 PRK10833, PRK10833, putative assembly protein; Provisional.
Length = 617
Score = 26.4 bits (59), Expect = 5.0
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 15 RGRLRDELRRALDVWSKHSK 34
R L+DE ++ L+ W++ +K
Sbjct: 583 RKHLQDEAKKRLNDWAERNK 602
>gnl|CDD|227710 COG5423, COG5423, Predicted metal-binding protein [Function
unknown].
Length = 167
Score = 26.0 bits (57), Expect = 5.3
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 17 RLRDELRRALDVWSKHSKLTFREVNDDRADILIYFEKENHWDGYPFDGPGKILAHAFFPG 76
+ E RRAL V K T + + + + E E G I AHA FPG
Sbjct: 63 EILKEYRRALLVKFKID--TSEDEEEKKRSLRKMLELEKE-----LFREGFIFAHALFPG 115
Query: 77 S 77
S
Sbjct: 116 S 116
>gnl|CDD|218717 pfam05724, TPMT, Thiopurine S-methyltransferase (TPMT). This
family consists of thiopurine S-methyltransferase
proteins from both eukaryotes and prokaryotes.
Thiopurine S-methyltransferase (TPMT) is a cytosolic
enzyme that catalyzes S-methylation of aromatic and
heterocyclic sulfhydryl compounds, including anticancer
and immunosuppressive thiopurines.
Length = 203
Score = 25.9 bits (57), Expect = 5.4
Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 4/47 (8%)
Query: 56 HWDGYPFDGPGKILAHAFFPGSGRGGDAHFDIDEDWMVLGVSRSANA 102
HWD P G+ D + ++ V+GV S A
Sbjct: 14 HWD----ALNLPPGLRVLVPLCGKALDMVWLAEQGHFVVGVEISELA 56
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 25.9 bits (57), Expect = 5.6
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 93 VLGVSRSANADEGK 106
VLGVSRSA+ DE K
Sbjct: 8 VLGVSRSADKDEIK 21
>gnl|CDD|238446 cd00874, RNA_Cyclase_Class_II, RNA 3' phosphate cyclase domain
(class II). These proteins function as RNA cyclase to
catalyze the ATP-dependent conversion of 3'-phosphate
to a 2'.3'-cyclic phosphodiester at the end of RNA
molecule. A conserved catalytic histidine residue is
found in all members of this subfamily.
Length = 326
Score = 26.0 bits (58), Expect = 6.4
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 72 AFFPGSGRGGDAHFDI 87
F PG +GGD FDI
Sbjct: 71 EFEPGKIKGGDYEFDI 86
>gnl|CDD|193466 pfam12993, DUF3877, Domain of unknown function, E. rectale Gene
description (DUF3877). Based on Eubacterium rectale
gene EUBREC_0237. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 175
Score = 25.3 bits (56), Expect = 7.1
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 26 LDVWSKHSK-LTFREVNDDRADILIYFEKENHWDGYPF---DGPGKILAHAFFP 75
LD++ +S + E+++ D LI FE E D Y + D I+ H F P
Sbjct: 115 LDLFHSYSDNVIIEEMDNGEFDYLIRFEDEPE-DPYYYCFKDEGCHIIYHRFLP 167
>gnl|CDD|150929 pfam10333, Pga1, GPI-Mannosyltransferase II co-activator. Pga1 is
found only in yeasts and not in mammals. It localises in
the ER as a glycosylated integral membrane protein. It
binds to the GPI-mannosyltransferase II subunit of the
GPI and it is responsible for the second mannose
addition to GPI precursors. The GPI-anchoring complex is
a glycolipid that functions as a membrane anchor for
many cell-surface proteins.
Length = 180
Score = 25.5 bits (56), Expect = 7.4
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 37 FREVNDDRADILIYFEKENHWDGYP 61
F+ D A I + F+ D YP
Sbjct: 107 FQGTWSDEARIYVTFKVVA--DSYP 129
>gnl|CDD|220568 pfam10099, RskA, Anti-sigma-K factor rskA. This domain, formerly
known as DUF2337, is the anti-sigma-K factor, RskA. In
Mycobacterium tuberculosis the protein positively
regulates expression of the antigenic proteins MPB70 and
MPB83.
Length = 171
Score = 25.4 bits (56), Expect = 7.5
Identities = 8/36 (22%), Positives = 10/36 (27%)
Query: 75 PGSGRGGDAHFDIDEDWMVLGVSRSANADEGKSLEL 110
D D + L + GK LEL
Sbjct: 73 ADGQPALVVSVDPDSGALTLVPLGAGAPPAGKVLEL 108
>gnl|CDD|179302 PRK01558, PRK01558, V-type ATP synthase subunit E; Provisional.
Length = 198
Score = 25.5 bits (56), Expect = 8.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 13 YDRGRLRDELRRALDVWSKHSKL 35
YD LR+ + R +D W K KL
Sbjct: 99 YDSNFLRELIIRVVDSWVKGDKL 121
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 25.7 bits (57), Expect = 8.5
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 93 VLGVSRSANADEGKS 107
+LGVS+ A+ +E K
Sbjct: 9 ILGVSKDASEEEIKK 23
>gnl|CDD|226384 COG3866, PelB, Pectate lyase [Carbohydrate transport and
metabolism].
Length = 345
Score = 25.6 bits (56), Expect = 8.9
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 75 PGSGRGGDAHFDIDEDWMVLGVSRSANADEGKSLELANAD-----EGRRHVT 121
SG GD DI +D + +S + D KS L ++D +G+ VT
Sbjct: 169 NASGSHGDGLVDIKKDANYITISYNKFHDHDKSSLLGSSDSSNYDDGKYKVT 220
>gnl|CDD|238138 cd00226, PRCH, Photosynthetic reaction center (RC) complex,
subunit H; RC is an integral membrane protein-pigment
complex which catalyzes light-induced reduction of
ubiquinone to ubiquinol, generating a transmembrane
electrochemical gradient of protons used to produce ATP
by ATP synthase. Subunit H is positioned mainly in the
cytoplasm with one transmembrane alpha helix. Provides
proton transfer pathway (water channels) connecting the
terminal quinone electron acceptor of RC, to the
aqueous phase. Found in photosynthetic bacteria: alpha,
beta, and gamma proteobacteria.
Length = 246
Score = 25.5 bits (56), Expect = 9.4
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 45 ADILIYFEKENHWDGYPFDGPG 66
A ++ Y +EN +GYP + P
Sbjct: 25 AGLIYYLRRENMREGYPLEDPD 46
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
0.320 0.140 0.443
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,716,677
Number of extensions: 614496
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 625
Number of HSP's successfully gapped: 44
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.2 bits)