RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6854
(148 letters)
>gnl|CDD|226318 COG3795, COG3795, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 123
Score = 29.3 bits (66), Expect = 0.45
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 43 RVMAEM----EELAKHGTFLPPDMLGLTDEQVEELKLRDDQGERCKPSG-YIENKDPIG 96
+MA + E LAK G P L T LR G+R G + E K+ +
Sbjct: 24 ALMAALGKYNERLAKAGVLGPGARLHPTTAAT---TLRFRGGKRTVIDGPFAETKEQLA 79
>gnl|CDD|237027 PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
Length = 508
Score = 29.3 bits (67), Expect = 0.69
Identities = 9/26 (34%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 31 ILNIYNGRLKVYRVMAE--MEELAKH 54
+L+++ G++ YR +AE +E+LA +
Sbjct: 353 LLSVFGGKITTYRKLAEHALEKLAPY 378
>gnl|CDD|133436 cd01666, TGS_DRG_C, TGS_DRG_C: DRG (developmentally regulated
GTP-binding protein) represents a family of GTP-binding
proteins that includes two members, DRG1 and DRG2. DRG1
and DRG2 have a C-terminal TGS domain (named after the
ThrRS, GTPase, and SpoT proteins where it occurs) with a
predominantly beta-sheet structure. The function of TGS
is unknown but its presence in two types of regulatory
proteins (the DRG GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 75
Score = 27.1 bits (61), Expect = 1.3
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 94 PIGRRNGYQPPIKMQDLIKTTIEEVKNKISKTLVER 129
P G+ + P+ ++ +T+E+V NKI K LV++
Sbjct: 8 PKGQEPDFDEPVILRR--GSTVEDVCNKIHKDLVKQ 41
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 27.5 bits (61), Expect = 1.8
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 21 STSIQQLLEEILNIYNGRLKVYRVMAEMEELAKHG----TFLPPDMLGLTDEQVEEL 73
S S+Q +E+L I N V+ +E L + G + G DE +EE
Sbjct: 105 SISLQSGDDEVLKIINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGENDEDLEET 161
>gnl|CDD|236989 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 28.0 bits (63), Expect = 1.9
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 37 GRLKVYRVMAEMEELAKHGTFLPPDMLGLTDEQVEELK 74
GR V++ E E + GTF+PP ++ L + +ELK
Sbjct: 979 GR-PVFQAARENSEDWQSGTFVPPTLIEL--DSFDELK 1013
>gnl|CDD|213289 cd05922, FACL_like_6, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 350
Score = 27.2 bits (61), Expect = 3.2
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 52 AKHGTFLPPDMLGLTDEQV------EELKLRDDQGERCKP 85
A T+LPP+ L + + EL + D+ G RC P
Sbjct: 155 AFRSTYLPPEELDRRPDSIGKAIPNVELWVVDEDGNRCAP 194
>gnl|CDD|237747 PRK14530, PRK14530, adenylate kinase; Provisional.
Length = 215
Score = 27.1 bits (60), Expect = 3.6
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 54 HGTFLPPDMLGLTDEQVEELKLRDDQGE---RCKPSGYIENKDPI----------GRRNG 100
H F P+ G+ DE EL RDD E R + + EN +P+ +G
Sbjct: 137 HVEFNQPEEEGVCDECGGELIQRDDDTEETVRERLDVFEENTEPVIEHYRDQGVLVEVDG 196
Query: 101 YQPPIKMQDLIKTTIEE 117
Q P ++ I+ I++
Sbjct: 197 EQTPDEVWADIQDAIDD 213
>gnl|CDD|181894 PRK09480, slmA, division inhibitor protein; Provisional.
Length = 194
Score = 26.7 bits (60), Expect = 4.2
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 131 QCLTEAVVQEGKGFGFDP 148
Q L EA ++EG GF D
Sbjct: 137 QILREAKLREGLGFDLDE 154
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 27.0 bits (61), Expect = 4.5
Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 2/19 (10%)
Query: 62 MLGLTDEQVEELKLRDDQG 80
GLT EQV+ +LR++ G
Sbjct: 350 YSGLTPEQVD--RLREEFG 366
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 27.0 bits (61), Expect = 4.7
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 28 LEEILNIYNGRLKVYRVMAEMEELAKHGTFLPPDMLGLTDEQVEELKLR 76
LE I+ Y + + E +E+ + + P+M + E+++EL+ R
Sbjct: 44 LEPIVEAYREYKQAQEDLEEAKEMLEEES--DPEMREMAKEELKELEER 90
>gnl|CDD|227096 COG4754, COG4754, Uncharacterized conserved protein [Function
unknown].
Length = 157
Score = 26.2 bits (58), Expect = 5.0
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 27 LLEEILNIYNGRLKVYRVMAEME 49
LL + NI+NGR + + EME
Sbjct: 17 LLYVLNNIFNGRADLPYLEKEME 39
>gnl|CDD|119388 cd00569, HTH_Hin_like, Helix-turn-helix domain of Hin and related
proteins, a family of DNA-binding domains unique to
bacteria and represented by the Hin protein of
Salmonella. The basic HTH domain is a simple fold
comprised of three core helices that form a
right-handed helical bundle. The principal DNA-protein
interface is formed by the third helix, the recognition
helix, inserting itself into the major groove of the
DNA. A diverse array of HTH domains participate in a
variety of functions that depend on their DNA-binding
properties. HTH_Hin represents one of the simplest
versions of the HTH domains; the characterization of
homologous relationships between various
sequence-diverse HTH domain families remains difficult.
The Hin recombinase induces the site-specific inversion
of a chromosomal DNA segment containing a promoter,
which controls the alternate expression of two genes by
reversibly switching orientation. The Hin recombinase
consists of a single polypeptide chain containing a
DNA-binding domain (HTH_Hin) and a catalytic domain.
Length = 42
Score = 24.3 bits (54), Expect = 7.5
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 65 LTDEQVEELKLRDDQGE 81
LT EQ+EE + GE
Sbjct: 6 LTPEQIEEARRLLAAGE 22
>gnl|CDD|197875 smart00788, Adenylsucc_synt, Adenylosuccinate synthetase.
Adenylosuccinate synthetase plays an important role in
purine biosynthesis, by catalyzing the GTP-dependent
conversion of IMP and aspartic acid to AMP.
Adenylosuccinate synthetase has been characterized from
various sources ranging from Escherichia coli (gene
purA) to vertebrate tissues. In vertebrates, two
isozymes are present - one involved in purine
biosynthesis and the other in the purine nucleotide
cycle. The crystal structure of adenylosuccinate
synthetase from E. coli reveals that the dominant
structural element of each monomer of the homodimer is a
central beta-sheet of 10 strands. The first nine strands
of the sheet are mutually parallel with right-handed
crossover connections between the strands. The 10th
strand is antiparallel with respect to the first nine
strands. In addition, the enzyme has two antiparallel
beta-sheets, comprised of two strands and three strands
each, 11 alpha-helices and two short 3/10-helices.
Further, it has been suggested that the similarities in
the GTP-binding domains of the synthetase and the p21ras
protein are an example of convergent evolution of two
distinct families of GTP-binding proteins. Structures of
adenylosuccinate synthetase from Triticum aestivum and
Arabidopsis thaliana when compared with the known
structures from E. coli reveals that the overall fold is
very similar to that of the E. coli protein.
Length = 417
Score = 26.3 bits (59), Expect = 7.8
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 65 LTDEQVEELKLRDDQGERCKPSGYIE----NKDPIGRRNGYQPPIKMQDLIKTTIEEV 118
L + ++ + ERC+P Y E +D G R+ P + I+ IEE+
Sbjct: 343 LDGKIIDYFPADLEDLERCEPI-YEELPGWKEDTTGVRSYEDLPENAKKYIE-RIEEL 398
>gnl|CDD|213365 cd12831, TmCorA-like_u2, Uncharacterized bacterial subfamily of the
Thermotoga maritima CorA-like family. This subfamily
belongs to the Thermotoga maritima CorA (TmCorA)-like
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes. Members of the
TmCorA-like family are found in all three kingdoms of
life. It is a functionally diverse family which includes
the CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, and three Saccharomyces cerevisiae
proteins: two located in the plasma membrane: the Mg2+
transporter Alr1p/Swc3p and the putative Mg2+
transporter, Alr2p, and the vacuole membrane protein
Mnr2p, a putative Mg2+ transporter. Thermotoga maritima
CorA forms funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 287
Score = 26.0 bits (58), Expect = 8.5
Identities = 9/35 (25%), Positives = 22/35 (62%)
Query: 17 ETSTSTSIQQLLEEILNIYNGRLKVYRVMAEMEEL 51
+ + +S ++L++E+ +I + LK+ R + M +L
Sbjct: 133 DNNVDSSNKKLMDEVFDIRSDLLKLRRTILPMRDL 167
>gnl|CDD|240017 cd04659, Piwi_piwi-like_ProArk, Piwi_piwi-like_ProArk: PIWI domain,
Piwi-like subfamily found in Archaea and Bacteria. RNA
silencing refers to a group of related gene-silencing
mechanisms mediated by short RNA molecules, including
siRNAs, miRNAs, and heterochromatin-related guide RNAs.
The central component of the RNA-induced silencing
complex (RISC) and related complexes is Argonaute. The
PIWI domain is the C-terminal portion of Argonaute and
consists of two subdomains, one of which provides the 5'
anchoring of the guide RNA and the other, the catalytic
site for slicing. This domain is also found in closely
related proteins, including the Piwi subfamily, where it
is believed to perform a crucial role in germline cells,
via a similar mechanism.
Length = 404
Score = 25.8 bits (57), Expect = 9.2
Identities = 10/44 (22%), Positives = 17/44 (38%)
Query: 86 SGYIENKDPIGRRNGYQPPIKMQDLIKTTIEEVKNKISKTLVER 129
G I PI + P ++DL+K +E + +R
Sbjct: 219 LGLILRGAPIEEPTEDRSPADLKDLLKRVLEGYRESHRGRDPKR 262
>gnl|CDD|233325 TIGR01238, D1pyr5carbox3, delta-1-pyrroline-5-carboxylate
dehydrogenase (PutA C-terminal domain). This model
represents one of several related branches of
delta-1-pyrroline-5-carboxylate dehydrogenase. Members
of this branch are the C-terminal domain of the PutA
bifunctional proline dehydrogenase /
delta-1-pyrroline-5-carboxylate dehydrogenase [Energy
metabolism, Amino acids and amines].
Length = 500
Score = 26.0 bits (57), Expect = 9.6
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 25 QQLLEEILNIYNGRLKVYRVMAEMEELAKHGTFLPPDMLGLTDEQVEELK 74
Q LL I ++ + K+ ++ + +HGTF+ P + L D + EL
Sbjct: 355 QNLLAHIEHMSQTQKKIAQLTLDDSRACQHGTFVAPTLFELDD--IAELS 402
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
0.315 0.136 0.383
Gapped
Lambda K H
0.267 0.0847 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,640,952
Number of extensions: 701313
Number of successful extensions: 709
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 35
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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: 42 (22.0 bits)
S2: 54 (24.4 bits)