RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4361
(122 letters)
>gnl|CDD|201590 pfam01085, HH_signal, Hedgehog amino-terminal signalling domain.
For the carboxyl Hint module, see pfam01079. Hedgehog is
a family of secreted signal molecules required for
embryonic cell differentiation.
Length = 160
Score = 117 bits (295), Expect = 5e-35
Identities = 54/78 (69%), Positives = 64/78 (82%), Gaps = 2/78 (2%)
Query: 34 GPGGKSGRRRYDRYKKITPLVYKQHVPNVSENTLTASGHSEGRISRDDKRFRDLIPNYNQ 93
GPG GRRR+ R K+TPLVYKQ +PNVSE TL ASG EG+I+RD +RF++L+PNYN
Sbjct: 1 GPGRGFGRRRHPR--KLTPLVYKQFIPNVSEKTLGASGRYEGKITRDSERFKELVPNYNP 58
Query: 94 DIIFKDDEGTGADRLMTQ 111
DIIFKD+E TGADRLMTQ
Sbjct: 59 DIIFKDEEKTGADRLMTQ 76
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 29.0 bits (66), Expect = 0.37
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 2 EKQEKKKKKKRKKKEK 17
EK EKK +K + K EK
Sbjct: 72 EKAEKKAEKAKAKAEK 87
Score = 25.2 bits (56), Expect = 7.6
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 3 KQEKKKKKKRKKKEKV 18
K EK K K KKK K
Sbjct: 77 KAEKAKAKAEKKKAKK 92
Score = 25.2 bits (56), Expect = 10.0
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 3 KQEKKKKKKRKKKEK 17
EK +KK K K K
Sbjct: 70 AWEKAEKKAEKAKAK 84
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 29.0 bits (65), Expect = 0.62
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 39 SGR--RRYDRYKKITPLVYKQHV--PNVSENTLTASGHSEGRISRDDK 82
+GR R++ R K+ + Y V PN S+N L + RI R D+
Sbjct: 283 TGRLIRKFLRRDKLLAVAYPSRVVLPNASKNALFLNTCIADRIGRYDR 330
>gnl|CDD|240386 PTZ00370, PTZ00370, STEVOR; Provisional.
Length = 296
Score = 28.8 bits (65), Expect = 0.69
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 87 LIPNYNQDIIFKDDEGTGADRLMTQLKNKMPHY 119
LI N Q K RL+ Q +N PHY
Sbjct: 28 LIQNNTQRTTIKS-------RLLAQTQNHNPHY 53
>gnl|CDD|204644 pfam11407, RestrictionMunI, Type II restriction enzyme MunI. Type
II restriction enzyme MunI recognises the palindromic
sequence C/AATTG. It makes contact with the DNA via the
major groove.
Length = 202
Score = 28.5 bits (63), Expect = 0.81
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 74 EGRISRDDKRFRDLIPNYN--QDIIFKDDEGTGADRLMTQLKNKMPHYAD 121
EG I+RD KR R++ Y+ QD F ++L+ K+ Y D
Sbjct: 153 EGDITRDPKRVREITFWYDHYQDNYFMWRPNESGEKLVQHFNEKLKKYLD 202
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 28.3 bits (64), Expect = 0.86
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 2 EKQEKKKKKKRKKKEK 17
K +KKK+K+ K K
Sbjct: 70 HKAQKKKEKQEAKAAK 85
>gnl|CDD|117583 pfam09017, Transglut_prok, Microbial transglutaminase. Microbial
transglutaminase (MTG) catalyzes an acyl transfer
reaction by means of a Cys-Asp diad mechanism, in which
the gamma-carboxyamide groups of peptide-bound glutamine
residues act as the acyl donors. The MTG molecule forms
a single, compact domain belonging to the alpha+beta
folding class, containing 11 alpha-helices and 8
beta-strands. The alpha-helices and the beta-strands are
concentrated mainly at the amino and carboxyl ends of
the polypeptide, respectively. These secondary
structures are arranged so that a beta-sheet is
surrounded by alpha-helices, which are clustered into
three regions.
Length = 414
Score = 27.7 bits (61), Expect = 1.5
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 55 YKQHVPNVSENTLTASGHSEGRISRDD-------KRFRDLIPNYNQDIIFKDDEGTGADR 107
YK + N EGRI++D KR R++ N+ + DEGT D
Sbjct: 173 YKNDLKNGRPRPGETRAEFEGRIAKDSFDEGKGFKRAREVASVMNKALENAHDEGTYIDN 232
Query: 108 LMTQLKNK 115
L T+L N
Sbjct: 233 LKTELANG 240
>gnl|CDD|224684 COG1770, PtrB, Protease II [Amino acid transport and metabolism].
Length = 682
Score = 27.6 bits (62), Expect = 1.7
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 25 IVLRESMCCGPGGKSGRRRYDRYKKIT 51
++L+ +M G GG SG R+ R ++I
Sbjct: 645 LLLKTNMDAGHGGASG--RFQRLEEIA 669
>gnl|CDD|222812 PHA00727, PHA00727, hypothetical protein.
Length = 278
Score = 27.1 bits (60), Expect = 2.1
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 3 KQEKKKKKKRKKKEKVYICV 22
K E KKKK+ KKEKV + V
Sbjct: 63 KAELSKKKKKFKKEKVDVRV 82
>gnl|CDD|233362 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
This model represents mitochondrial forms of the TCA
cycle enzyme aconitate hydratase, also known as
aconitase and citrate hydro-lyase [Energy metabolism,
TCA cycle].
Length = 745
Score = 26.8 bits (59), Expect = 3.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 53 LVYKQHVPNVSENTLTASGHSE 74
L YK H+ N+S NTL + ++E
Sbjct: 572 LKYKGHLDNISNNTLIGAVNAE 593
>gnl|CDD|222379 pfam13786, DUF4179, Domain of unknown function (DUF4179).
Length = 93
Score = 25.7 bits (57), Expect = 3.5
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 6 KKKKKKRKKKEKVYICVMCIVL 27
KK KKKRKKK+K+ IV
Sbjct: 1 KKVKKKRKKKKKIAAAAALIVT 22
Score = 24.5 bits (54), Expect = 8.9
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 5 EKKKKKKRKKKEKVYICVMCIVL 27
+K KKK++KKK+ + + +
Sbjct: 1 KKVKKKRKKKKKIAAAAALIVTV 23
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 26.1 bits (58), Expect = 3.8
Identities = 5/24 (20%), Positives = 13/24 (54%)
Query: 1 MEKQEKKKKKKRKKKEKVYICVMC 24
+ + +R ++ KV++C +C
Sbjct: 117 RHAEMFRGLLERLEEGKVWVCPVC 140
>gnl|CDD|226584 COG4099, COG4099, Predicted peptidase [General function prediction
only].
Length = 387
Score = 26.4 bits (58), Expect = 4.2
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 5/73 (6%)
Query: 44 YDRYKKITPLVYKQH-VPNVSENTLTASGHSEGRISRDDKRFRDLI--PNYNQDIIFKDD 100
Y KK PLV H + G I+ + + P YN IF D
Sbjct: 184 YAPDKKYYPLVLFLHGAGQGGSDNDKVLSSGIGAIAWAGPEDQCFVLAPQYNP--IFADS 241
Query: 101 EGTGADRLMTQLK 113
E L+ ++
Sbjct: 242 EEKTLLYLIEKID 254
>gnl|CDD|176532 cd08590, PI-PLCc_Rv2075c_like, Catalytic domain of uncharacterized
Mycobacterium tuberculosis Rv2075c-like proteins. This
subfamily corresponds to the catalytic domain present in
uncharacterized Mycobacterium tuberculosis Rv2075c and
its homologs. Members in this family are more closely
related to the Streptomyces antibioticus
phosphatidylinositol-specific phospholipase
C1(SaPLC1)-like proteins rather than the typical
bacterial phosphatidylinositol-specific phospholipase C
(PI-PLC, EC 4.6.1.13), which participate in
Ca2+-independent PI metabolism, hydrolyzing the membrane
lipid phosphatidylinositol (PI) to produce
phosphorylated myo-inositol and diacylglycerol (DAG). In
contrast, SaPLC1-like proteins have two Ca2+-chelating
amino acid substitutions which convert them to
metal-dependent bacterial PI-PLC. Rv2075c and its
homologs have the same amino acid substitutions as well,
which might suggest they have metal-dependent PI-PLC
activity.
Length = 267
Score = 26.2 bits (58), Expect = 4.6
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 11/59 (18%)
Query: 69 ASGHSEGRISRDDKRFRDLIP------NYNQD---IIFKDD--EGTGADRLMTQLKNKM 116
G S +D+ F D + N N D I++ +D +G D L L +
Sbjct: 75 GDHGYLGVCSSEDRLFEDGLNEIADWLNANPDEVVILYLEDHGDGGKDDELNALLNDAF 133
>gnl|CDD|237371 PRK13381, PRK13381, peptidase T; Provisional.
Length = 404
Score = 26.4 bits (59), Expect = 4.8
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 11/45 (24%)
Query: 84 FRDLIPNYNQDIIFKDDEGT---GADR------LMTQLKNKMPHY 119
+L+ +DIIF D GT GAD +MT L+N +
Sbjct: 115 HPELLNYQGEDIIFSD--GTSVLGADNKAAIAVVMTLLENLTENE 157
>gnl|CDD|177130 MTH00058, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 293
Score = 26.0 bits (58), Expect = 5.0
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 21 CVMCIVLRESMCCG 34
C MCIV+ +C G
Sbjct: 146 CFMCIVIFCGLCYG 159
>gnl|CDD|114900 pfam06208, BDV_G, Borna disease virus G protein. This family
consists of Borna disease virus G glycoprotein
sequences. Borna disease virus (BDV) infection produces
a variety of clinical diseases, from behavioural
illnesses to classical fatal encephalitis. G protein is
important for viral entry into the host cell.
Length = 503
Score = 26.2 bits (57), Expect = 5.0
Identities = 20/71 (28%), Positives = 28/71 (39%)
Query: 34 GPGGKSGRRRYDRYKKITPLVYKQHVPNVSENTLTASGHSEGRISRDDKRFRDLIPNYNQ 93
G G K R RY++ L + N++ ASGH I+ DL+P
Sbjct: 377 GSGVKPKRIRYNKTSHDYHLEEFEASLNMTPQLDIASGHETDPINHAYGTQADLLPYTRS 436
Query: 94 DIIFKDDEGTG 104
I D G+G
Sbjct: 437 SNITSTDTGSG 447
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 26.0 bits (58), Expect = 5.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 4 QEKKKKKKRKKKEKVYICV 22
Q K KK K+ KK K +
Sbjct: 342 QRKSKKYKKNKKNKWTKAL 360
>gnl|CDD|143437 cd07119, ALDH_BADH-GbsA, Bacillus subtilis NAD+-dependent betaine
aldehyde dehydrogenase-like. Included in this CD is the
NAD+-dependent, betaine aldehyde dehydrogenase (BADH,
GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the
synthesis of the osmoprotectant glycine betaine from
choline or glycine betaine aldehyde.
Length = 482
Score = 26.1 bits (58), Expect = 6.4
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 77 ISRDDKRFRDLIPNYNQDIIFKDDEGTGAD 106
+ + RD+I N ++I EGT D
Sbjct: 7 VEAASGKTRDIINPANGEVIATVPEGTAED 36
>gnl|CDD|212594 cd11720, FANCI, Fanconi anemia I protein. The Fanconi anemia ID
complex consists of two subunits, Fanconi anemia I and
Fanconi anemia D2 (FANCI-FANCD2) and plays a central role
in the repair of DNA interstrand cross-links (ICLs). The
complex is activated via DNA damage-induced
phosphorylation by ATR (ataxia telangiectasia and
Rad3-related) and monoubiquitination by the FA core
complex ubiquitin ligase, and it binds to DNA at the ICL
site, recognizing branched DNA structures. Defects in the
complex cause Fanconi anemia, a cancer predisposition
syndrome. The phosphorylation of FANCI may function as a
molecular switch to turn on the FA pathway.
Length = 1202
Score = 26.1 bits (58), Expect = 6.8
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 2 EKQEKKKKKKRKKKEKVYICVMCIVLRESMC 32
E Q ++ KK+KKK K +LRE+
Sbjct: 1130 ENQSEQDSKKKKKKAKSK-VQRNKILRETKL 1159
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 25.9 bits (58), Expect = 6.9
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 5/24 (20%)
Query: 82 KRFRDLIPNYNQDIIFKDDEGTGA 105
+R+RD I +N DI +GTGA
Sbjct: 258 ERYRDEICTFNDDI-----QGTGA 276
>gnl|CDD|150277 pfam09548, Spore_III_AB, Stage III sporulation protein AB
(spore_III_AB). SpoIIIAB represents the stage III
sporulation protein AB, which is encoded in a spore
formation operon: spoIIIAABCDEFGH that is under sigma G
regulation. A comparative genome analysis of all
sequenced genomes of Firmicutes shows that the proteins
are strictly conserved among the sub-set of
endospore-forming species.
Length = 170
Score = 25.6 bits (57), Expect = 7.7
Identities = 8/19 (42%), Positives = 17/19 (89%)
Query: 1 MEKQEKKKKKKRKKKEKVY 19
+E+QE++ ++++KK EK+Y
Sbjct: 136 LERQEEEAEEEQKKNEKMY 154
>gnl|CDD|206208 pfam14038, YqzE, YqzE-like protein. The YqzE-like protein family
includes the B. subtilis YqzE protein, which is
functionally uncharacterized. It is a part of the ComG
operon, which is regulated by the competence
transcription factor ComK. This family of proteins is
found in bacteria. Proteins in this family are
typically between 49 and 66 amino acids in length.
Length = 54
Score = 24.2 bits (53), Expect = 8.5
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 3 KQEKKKKKKRKKKEK 17
K+E+K+KK+ +K+EK
Sbjct: 21 KEERKEKKEERKEEK 35
>gnl|CDD|214819 smart00793, AgrB, Accessory gene regulator B. The accessory gene
regulator (agr) of Staphylococcus aureus is the central
regulatory system that controls the gene expression for
a large set of virulence factors. The arg locus consists
of two transcripts: RNAII and RNAIII. RNAII encodes four
genes (agrA, B, C, and D) whose gene products assemble a
quorum sensing system. At low cell density, the agr
genes are continuously expressed at basal levels. A
signal molecule, autoinducing peptide (AIP), produced
and secreted by the bacteria, accumulates outside of the
cells. When the cell density increases and the AIP
concentration reaches a threshold, it activates the agr
response, i.e. activation of secreted protein gene
expression and subsequent repression of cell
wall-associated protein genes. AgrB and AgrD are
essential for the production of the autoinducing peptide
which functions as a signal for quorum sensing. AgrB is
a transmembrane protein. AgrB is involved in the
proteolytic processing of AgrD and may have both
proteolytic enzyme activity and a transporter
facilitating the export of the processed AgrD peptide.
Length = 184
Score = 25.3 bits (56), Expect = 9.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 2 EKQEKKKKKKRKKKEKVYICVMCIVL 27
EKQ +K +KK +K I + I++
Sbjct: 124 EKQPVIPEKLKKKLKKKSIILSLILI 149
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 25.7 bits (57), Expect = 9.1
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 2 EKQEKKKKKKRKKKEK 17
EK+EK+K+K + KK
Sbjct: 401 EKKEKEKEKPKVKKRH 416
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 0.135 0.397
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,258,256
Number of extensions: 548199
Number of successful extensions: 1759
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1680
Number of HSP's successfully gapped: 139
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (21.6 bits)
S2: 53 (24.1 bits)