RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1958
(202 letters)
>gnl|CDD|239565 cd03483, MutL_Trans_MLH1, MutL_Trans_MLH1: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH1 (MutL homologue
1). This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. MLH1 forms
heterodimers with PMS2, PMS1 and MLH3. These three
complexes have distinct functions in meiosis.
hMLH1-hPMS2 also participates in the repair of all DNA
mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1
or hMLH1-hMLH3 in MMR have not been established. Cells
lacking hMLH1 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hMLH1 causes predisposition to HNPCC, Muir-Torre
syndrome and Turcot syndrome (HNPCC variant). Mutation
in hMLH1 accounts for a large fraction of HNPCC
families.
Length = 127
Score = 59.6 bits (145), Expect = 8e-12
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 6 VNVHPTKHEVHFLHEDTIIERVQSMLEKTLL 36
VNVHPTK EVHFL+E+ IIER+Q ++E L
Sbjct: 97 VNVHPTKREVHFLNEEEIIERIQKLVEDKLS 127
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 61.2 bits (149), Expect = 3e-11
Identities = 36/200 (18%), Positives = 66/200 (33%), Gaps = 16/200 (8%)
Query: 6 VNVHPTKHEVHFLHEDTIIER----VQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTK 61
VNVHP K EV F E + + ++ L + L S P + + P+
Sbjct: 301 VNVHPAKKEVRFSDERLVHDLIYEAIKEALAQQGLIPPASVEAPKSASQPLPAFQEPSPL 360
Query: 62 AKPSSTSSNTNNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQRATSKQTSNKKYKRRE 121
+ S + ++ + A + + S + +
Sbjct: 361 PESRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIR----PLSKNILPESSPGSLK 416
Query: 122 IKLSSVRDLRGEIEKQKSSQLC--------EVFRKLSFVGCATPCMCLIQHETKLYIVNV 173
+ S DL E + + Q +VF +G L +HE L +V+
Sbjct: 417 NEDRSYDDLLEEPAESEDKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDGLVLVDQ 476
Query: 174 TYVLEELFYQLMLHDFGNFG 193
E + Y+ + ++ GN G
Sbjct: 477 HAAHERILYEKLKNELGNVG 496
>gnl|CDD|201604 pfam01119, DNA_mis_repair, DNA mismatch repair protein, C-terminal
domain. This family represents the C-terminal domain of
the mutL/hexB/PMS1 family. This domain has a ribosomal
S5 domain 2-like fold.
Length = 119
Score = 52.9 bits (128), Expect = 2e-09
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 6 VNVHPTKHEVHFLHEDTIIERVQSMLEKTLL 36
VNVHP K EV F E + + ++ + + L
Sbjct: 89 VNVHPAKREVRFRDEREVHDFIEEAVREALA 119
>gnl|CDD|238405 cd00782, MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of DNA mismatch repair
(MutL/MLH1/PMS2) family. This transducer domain is
homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. Included in this group are
proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and
E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1
and MLH3. These three complexes have distinct functions
in meiosis. hMLH1-hPMS2 also participates in the repair
of all DNA mismatch repair (MMR) substrates. Roles for
hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been
established. Cells lacking either hMLH1 or hPMS2 have a
strong mutator phenotype and display microsatellite
instability (MSI). Mutation in hMLH1 causes
predisposition to HNPCC, Muir-Torre syndrome and Turcot
syndrome (HNPCC variant). Mutation in hPMS2 causes
predisposition to HPNCC and Turcot syndrome. Mutation in
hMLH1 accounts for a large fraction of HNPCC families.
There is no convincing evidence to support hPMS1 having
a role in HNPCC predisposition. It has been suggested
that hMLH3 may be a low risk gene for colorectal cancer;
however there is little evidence to support it having a
role in classical HNPCC. It has been suggested that
during initiation of DNA mismatch repair in E. coli, the
mismatch recognition protein MutS recruits MutL in the
presence of ATP. The MutS(ATP)-MutL ternary complex
formed, then recruits the latent endonuclease MutH.
Length = 122
Score = 52.9 bits (128), Expect = 3e-09
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 6 VNVHPTKHEVHFLHEDTIIERVQSMLEKTL 35
VNVHPTK EV F E+ ++E ++ L L
Sbjct: 93 VNVHPTKREVRFSDEEEVLELIREALRSAL 122
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 47.5 bits (114), Expect = 2e-06
Identities = 30/189 (15%), Positives = 63/189 (33%), Gaps = 8/189 (4%)
Query: 6 VNVHPTKHEVHFLHEDTIIERVQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAKPS 65
VNVHP KHEV F E + + + +++ L S + A+P
Sbjct: 296 VNVHPAKHEVRFRDERLVHDLIVQAIQEALAQSGLI--------PAAAGANQVLEPAEPE 347
Query: 66 STSSNTNNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQRATSKQTSNKKYKRREIKLS 125
+ + + A ++ + + A++ S + +
Sbjct: 348 PLPLQQTPLYASGSSPPASSPSSAPPEQSEESQEESSAEKNPLQPNASQSEAAAAASAEA 407
Query: 126 SVRDLRGEIEKQKSSQLCEVFRKLSFVGCATPCMCLIQHETKLYIVNVTYVLEELFYQLM 185
+ E ++++ + F +G L ++E LY+V+ E L Y+ +
Sbjct: 408 AAAAPAAAPEPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQL 467
Query: 186 LHDFGNFGV 194
G+
Sbjct: 468 KDKLAEVGL 476
>gnl|CDD|239564 cd03482, MutL_Trans_MutL, MutL_Trans_MutL: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to Escherichia coli MutL. EcMutL
belongs to the DNA mismatch repair (MutL/MLH1/PMS2)
family. This transducer domain is homologous to the
second domain of the DNA gyrase B subunit, which is
known to be important in nucleotide hydrolysis and the
transduction of structural signals from the ATP-binding
site to the DNA breakage/reunion regions of the enzymes.
It has been suggested that during initiation of DNA
mismatch repair in E. coli, the mismatch recognition
protein MutS recruits MutL in the presence of ATP. The
MutS(ATP)-MutL ternary complex formed, then recruits the
latent endonuclease MutH. Prokaryotic MutS and MutL are
homodimers.
Length = 123
Score = 35.3 bits (82), Expect = 0.005
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 6/31 (19%)
Query: 6 VNVHPTKHEVHF-----LHEDTIIERVQSML 31
VNVHP KHEV F +H D I V+ L
Sbjct: 93 VNVHPAKHEVRFRDSRLVH-DFIYHAVKKAL 122
>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General
function prediction only].
Length = 872
Score = 34.1 bits (78), Expect = 0.042
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 29 SMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPA 81
S T + T+ V T+T + +T + + +S + + +TTTTT+P+
Sbjct: 790 SAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTTSPS 842
Score = 29.8 bits (67), Expect = 1.1
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 22 TIIERVQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTT 79
+ ++E T + T V TQT S S T+ + S++++ T + + TTT
Sbjct: 790 SAYSNTSILIETTSV-VITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTTSPSQTTT 846
>gnl|CDD|203622 pfam07355, GRDB, Glycine/sarcosine/betaine reductase selenoprotein
B (GRDB). This family represents a conserved region
approximately 350 residues long within the selenoprotein
B component of the bacterial glycine, sarcosine and
betaine reductase complexes.
Length = 349
Score = 33.1 bits (76), Expect = 0.070
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 9 HPTKHEVHFLHEDTIIERVQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPT------TKA 62
P V++ HE+ +R ML K L G F T+ +P F PP +KA
Sbjct: 173 IPRGIRVNYFHEERGAKRAVDMLVKKLKGEE----FQTEYPMPVFDRVPPNPAVKDLSKA 228
Query: 63 K 63
K
Sbjct: 229 K 229
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families.
Length = 107
Score = 30.7 bits (70), Expect = 0.16
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 2 DQPPVNVHPTKHEVH 16
VNVHPTK EV
Sbjct: 93 SLVDVNVHPTKEEVR 107
>gnl|CDD|239567 cd03485, MutL_Trans_hPMS_1_like, MutL_Trans_hPMS1_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM1 (hPSM1) and yeast
MLH2. hPSM1 and yMLH2 are members of the DNA mismatch
repair (MutL/MLH1/PMS2) family. This transducer domain
is homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. PMS1 forms a heterodimer with
MLH1. The MLH1-PMS1 complex functions in meiosis. Loss
of yMLH2 results in a small but significant decrease in
spore viability and a significant increase in gene
conversion frequencies. A role for hMLH1-hPMS1 in DNA
mismatch repair has not been established. Mutation in
hMLH1 accounts for a large fraction of Lynch syndrome
(HNPCC) families, however there is no convincing
evidence to support hPMS1 having a role in HNPCC
predisposition.
Length = 132
Score = 31.1 bits (71), Expect = 0.19
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 6 VNVHPTKHEVHFLHEDTIIERVQSMLEKTL 35
VN+ P K +V +++ +++ V+++LE
Sbjct: 102 VNIEPDKDDVLLQNKEAVLQAVENLLESLY 131
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 30.5 bits (68), Expect = 0.65
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 34 TLLGSNTSRVFYTQTKLPSFSTEPP-TTKAKPSSTSSNTNNTTTTTTP 80
+ G+NT Q +L + S+ P TT P S+SS+++ + +T+P
Sbjct: 1212 GMSGTNTFTFKAAQLQLSAASSPPAATTPTPPPSSSSSSSAQSISTSP 1259
>gnl|CDD|233367 TIGR01349, PDHac_trf_mito, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model represents one of several closely related clades
of the dihydrolipoamide acetyltransferase subunit of the
pyruvate dehydrogenase complex. It includes sequences
from mitochondria and from alpha and beta branches of
the proteobacteria, as well as from some other bacteria.
Sequences from Gram-positive bacteria are not included.
The non-enzymatic homolog protein X, which serves as an
E3 component binding protein, falls within the clade
phylogenetically but is rejected by its low score
[Energy metabolism, Pyruvate dehydrogenase].
Length = 436
Score = 29.4 bits (66), Expect = 1.3
Identities = 22/75 (29%), Positives = 30/75 (40%)
Query: 63 KPSSTSSNTNNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQRATSKQTSNKKYKRREI 122
P+S + TT T PA V T + E + K IA + SKQT Y E
Sbjct: 181 SPASANQQAAATTPATYPAAAPVSTGSYEDVPLSNIRKIIAKRLLESKQTIPHYYVSIEC 240
Query: 123 KLSSVRDLRGEIEKQ 137
+ + LR E+
Sbjct: 241 NVDKLLALRKELNAM 255
>gnl|CDD|216513 pfam01456, Mucin, Mucin-like glycoprotein. This family of
trypanosomal proteins resemble vertebrate mucins. The
protein consists of three regions. The N and C terminii
are conserved between all members of the family, whereas
the central region is not well conserved and contains a
large number of threonine residues which can be
glycosylated. Indirect evidence suggested that these
genes might encode the core protein of parasite mucins,
glycoproteins that were proposed to be involved in the
interaction with, and invasion of, mammalian host cells.
This family contains an N-terminal signal peptide.
Length = 143
Score = 28.3 bits (62), Expect = 1.9
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 3/79 (3%)
Query: 47 QTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQR 106
QT + +T PPTT ++T++ T TTTTT T + SK
Sbjct: 44 QTTTTTTTTTPPTT---TTTTTTTTTTITTTTTKTTTTTTTTTTTTTTTEAPSKNTTTSE 100
Query: 107 ATSKQTSNKKYKRREIKLS 125
A + + REI S
Sbjct: 101 APTTTDTRAPSSIREIDGS 119
Score = 26.0 bits (56), Expect = 9.3
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 46 TQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPA 81
T T + +T TT ++T++ T TTTTTT A
Sbjct: 56 TTTTTTTTTTTTITTTTTKTTTTTTTTTTTTTTTEA 91
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 312
Score = 28.8 bits (65), Expect = 2.1
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 6 VNVHPTKHEVH 16
VNVHP K EV
Sbjct: 302 VNVHPDKKEVR 312
>gnl|CDD|223704 COG0631, PTC1, Serine/threonine protein phosphatase [Signal
transduction mechanisms].
Length = 262
Score = 28.5 bits (64), Expect = 2.4
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 119 RREIKLSSVRDLRGEIEKQKSSQLCEVFRKLS--------FVGCATPCMCLIQHETKLYI 170
R ++ L +E+ + + ++ G T + L+ KLY+
Sbjct: 65 ARLFDETNFNSLNESLEELLKEAILKANEAIAEEGQLNEDVRGMGTTLVLLLIRGNKLYV 124
Query: 171 VNV----TYVL-EELFYQL 184
NV Y+L + QL
Sbjct: 125 ANVGDSRAYLLRDGELKQL 143
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or
lesions in the genetic loci have been linked to the
aetiology of asthma, bronchiectasis, chronic obstructive
pulmonary disease etc. Disease-causing mutations have
been studied by 36Cl efflux assays in vitro cell
cultures and electrophysiology, all of which point to
the impairment of chloride channel stability and not the
biosynthetic processing per se [Transport and binding
proteins, Anions].
Length = 1490
Score = 28.7 bits (64), Expect = 2.5
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 12/87 (13%)
Query: 25 ERVQSMLEKTL----LGSNTSRVFYTQTKLPSFSTEPPTTKAKPSST------SSNTNNT 74
ER S+L +TL + +++ +T SF PP K + +S +
Sbjct: 657 ERRNSILTETLRRVSIDGDSTVFSGPETIKQSFKQPPPEFAEKRKQSIILNPIASARKFS 716
Query: 75 TTTTTPAYKLVRT--DASEQKLDRFLS 99
P T DA + +R S
Sbjct: 717 FVQMGPQKAQATTIEDAVREPSERKFS 743
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 28.0 bits (62), Expect = 4.1
Identities = 20/112 (17%), Positives = 48/112 (42%), Gaps = 3/112 (2%)
Query: 32 EKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTP--AYKLVRTDA 89
EK L S++S + SF + P + + S++ S+ ++ + + +D
Sbjct: 118 EKHNLDSSSSSSISSSLTNISFFSSPTSIYSCLSNSLSSKHSPKVIKENQSTHVNISSDN 177
Query: 90 SEQKLDRFLSKYIADQRATSKQTSNKKYKRREIKLSSVRDLRGEIEKQKSSQ 141
S + + +K + Q + T K +R S++++ + K+K+ +
Sbjct: 178 SPRNKEI-SNKQLKKQTNVTHTTCYDKMRRSPRNTSTIKNNTNDKNKEKNKE 228
>gnl|CDD|215397 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase
component of pyruvate dehydrogenase complex.
Length = 539
Score = 27.9 bits (62), Expect = 4.8
Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 1/64 (1%)
Query: 51 PSFSTEPPTTKAKPSSTSSN-TNNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQRATS 109
PS S P KAKPS ++P K + A DR + +A + A
Sbjct: 202 PSSSAAPAAPKAKPSPPPPKEEEVEKPASSPEPKASKPSAPPSSGDRIFASPLARKLAED 261
Query: 110 KQTS 113
Sbjct: 262 NNVP 265
>gnl|CDD|226444 COG3934, COG3934, Endo-beta-mannanase [Carbohydrate transport and
metabolism].
Length = 587
Score = 27.6 bits (61), Expect = 6.3
Identities = 7/44 (15%), Positives = 19/44 (43%)
Query: 72 NNTTTTTTPAYKLVRTDASEQKLDRFLSKYIADQRATSKQTSNK 115
NN + +++ +A E K +++++I +K +
Sbjct: 320 NNWKDISMCSFQPPTYEAGEIKPRDYVAQHIFVAERLNKPLFIR 363
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 27.5 bits (60), Expect = 6.3
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 46 TQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPA 81
T+ P+ + T K ++ ++ N T T+TP+
Sbjct: 299 TEAAKPAPAPSTNTNANKTNTNTNTNTNNTNTSTPS 334
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 27.6 bits (61), Expect = 6.3
Identities = 22/125 (17%), Positives = 35/125 (28%), Gaps = 12/125 (9%)
Query: 4 PPVNVHPTKHEVHFLHEDTIIERVQSMLEKTLLGSNTSRVFYTQTKLPSFSTEPPTTKAK 63
PVNV IE+ L + +N R T +
Sbjct: 71 APVNVQTLASPQ--------IEKAWHALSSLSINNNYLRPGKTPPIDNGSTDLSSDVGQS 122
Query: 64 PSSTSSNTNNTTTTTT-PAYKLVRTDASEQKLDRFLSKYIADQRATSKQTSNKKYKRREI 122
+ SS+T + P + F S + D AT+++ EI
Sbjct: 123 TTKVSSSTGGSYYEHNHPHQNQREVSGTNSSFASFSSSSVGDDNATAEKVPRGNS---EI 179
Query: 123 KLSSV 127
+ S
Sbjct: 180 RASVP 184
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed.
Length = 592
Score = 27.4 bits (60), Expect = 6.4
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 46 TQTKLPSFSTEPPTTKAKP---SSTSSNTNNTTTTTTPA-YKLVRTDA 89
QTK P K +T SN +N T+++TPA Y L++ A
Sbjct: 96 EQTKTPEEKQPAAKQVEKAPAEPATVSNPDNATSSSTPATYNLLQKSA 143
>gnl|CDD|234504 TIGR04216, halo_surf_glyco, major cell surface glycoprotein.
Members of this family are the S-layer-forming
halobacterial major cell surface glycoprotein. The
highest scores below model cutoffs are fragmentary
paralogs to actual members of the family. Modifications
include at N-linked and O-linked glycosylation, a
C-terminal diphytanylglyceryl modification, and probable
cleavage of the PGF-CTERM tail.
Length = 782
Score = 27.2 bits (60), Expect = 6.6
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 37 GSNTSRVFYT---QTKLPSFST-EPPTTKAKPSSTSSNTNNTTTTTTP 80
G NT RV +T+ P +T E PTT P++T TT T P
Sbjct: 697 GDNTDRVNVEVVEETERPDTTTSEDPTTTTTPTTTG--PEETTETAEP 742
>gnl|CDD|180584 PRK06481, PRK06481, fumarate reductase flavoprotein subunit;
Validated.
Length = 506
Score = 26.7 bits (59), Expect = 8.7
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 60 TKAKPSSTSSNTNNTTTTTTPAYKLVRTDASEQK 93
T +K S+SS + T T+ A K TD SE K
Sbjct: 26 TTSKSDSSSSKESEKTEVTSGASKTSYTDPSELK 59
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 26.8 bits (59), Expect = 9.2
Identities = 20/105 (19%), Positives = 41/105 (39%), Gaps = 4/105 (3%)
Query: 46 TQTKLPSFSTEPPTTKAKPSSTSSNTNNTTTTTTPAYK----LVRTDASEQKLDRFLSKY 101
T K + +P KA S ++ T T TT+ V+ S + + ++
Sbjct: 7 TTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVTVK 66
Query: 102 IADQRATSKQTSNKKYKRREIKLSSVRDLRGEIEKQKSSQLCEVF 146
+ K++ KK ++E + V + ++ K S ++F
Sbjct: 67 FEKTESVKKESVAKKTVKKEAVSAEVFEASNKLFKNTSKLPKKLF 111
>gnl|CDD|234428 TIGR03979, His_Ser_Rich, His-Xaa-Ser repeat protein HxsA. Members
of this protein share two defining regions. One is a
histidine/serine-rich cluster, typically
H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in
the context of a pair of radical SAM proteins, HxsB and
HxsC, and a fourth protein HxsD. The system is predicted
to perform peptide modifications, likely in the
His-Xaa-Ser region, to produce some uncharacterized
natural product.
Length = 186
Score = 26.4 bits (58), Expect = 9.9
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 3/59 (5%)
Query: 37 GSNTSRVFYTQTKLPSFSTEPPTTKAKPSSTSSNTN-NTTTTTTPAYKLVRTDASEQKL 94
+ V T S+ P+ PS SS + +TT P ++ ++KL
Sbjct: 72 AGGSYSVPSGDTSTYSYPV--PSPSYSPSPGSSIQSLPSTTGVRPQSSAENANSEKRKL 128
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
0.317 0.130 0.370
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,450,160
Number of extensions: 790666
Number of successful extensions: 1174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1106
Number of HSP's successfully gapped: 56
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.5 bits)