RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032430
(141 letters)
>gnl|CDD|223131 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 64.6 bits (158), Expect = 3e-13
Identities = 26/60 (43%), Positives = 41/60 (68%)
Query: 6 QGCHRLRGRRAGSSLYLDVHIVVDPFSSVSAAHGVGENVRHQIHKSHPEVSEVFIHIDPA 65
+G H LR R++GS +++DVHI VDP S+ AH + + V +I K P+V++V IH++P
Sbjct: 231 KGVHDLRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFPKVADVTIHVEPL 290
>gnl|CDD|233348 TIGR01297, CDF, cation diffusion facilitator family transporter.
This model describes a broadly distributed family of
transporters, a number of which have been shown to
transport divalent cations of cobalt, cadmium and/or
zinc. The family has six predicted transmembrane
domains. Members of the family are variable in length
because of variably sized inserts, often containing
low-complexity sequence [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 268
Score = 59.5 bits (145), Expect = 2e-11
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 6 QGCHRLRGRRAGSS-LYLDVHIVVDPFSSVSAAHGVGENVRHQIHKSHPEVSEVFIHIDP 64
+G H L R G L+LDVH+VVDP + AH + + +I K HP + V I ++P
Sbjct: 208 KGVHDLHIWRIGPGKLFLDVHVVVDPDLDLKQAHDIALEIEREILKRHPGIEHVTIQVEP 267
Query: 65 A 65
Sbjct: 268 C 268
>gnl|CDD|216561 pfam01545, Cation_efflux, Cation efflux family. Members of this
family are integral membrane proteins, that are found to
increase tolerance to divalent metal ions such as
cadmium, zinc, and cobalt. These proteins are thought to
be efflux pumps that remove these ions from cells.
Length = 273
Score = 55.8 bits (135), Expect = 4e-10
Identities = 20/60 (33%), Positives = 36/60 (60%)
Query: 7 GCHRLRGRRAGSSLYLDVHIVVDPFSSVSAAHGVGENVRHQIHKSHPEVSEVFIHIDPAY 66
G H LR ++G ++D+HI VDP +V AH + + + + + P +++V IH++PA
Sbjct: 211 GVHDLRVWKSGPKYFVDIHIEVDPDLTVEEAHEIADEIERALKEKFPGIADVTIHVEPAP 270
>gnl|CDD|181919 PRK09509, fieF, ferrous iron efflux protein F; Reviewed.
Length = 299
Score = 36.6 bits (85), Expect = 0.002
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 6 QGCHRLRGRRAGSSLYLDVHIVVDPFSSVSAAHGVGENVRHQIHKSHPEVSEVFIHIDP 64
G H LR R++G + ++ +H+ ++ + AH + + V + + P S+V IH DP
Sbjct: 229 SGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFPG-SDVIIHQDP 286
>gnl|CDD|100066 cd02637, R3H_PARN, R3H domain of Poly(A)-specific ribonuclease
(PARN). PARN is a poly(A)-specific 3' exonuclease from
the RNase D family that, in Xenopus, deadenylates a
specific class of maternal mRNAs which results in their
translational repression. The name of the R3H domain
comes from the characteristic spacing of the most
conserved arginine and histidine residues. The function
of the domain is predicted to bind ssDNA or ssRNA.
Length = 65
Score = 33.1 bits (76), Expect = 0.007
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 10/50 (20%)
Query: 69 FSPSTMDQLGLEGCKAHSSNICVDDLDIDAVVYNTLSTKFPEKMGVERIT 118
F S D L LE C ++Y TL K+P+ + VE +
Sbjct: 11 FLESEEDDLELEPCNGF----------QRKLIYQTLEQKYPKGIHVETLE 50
>gnl|CDD|236761 PRK10795, PRK10795, penicillin-binding protein 2; Provisional.
Length = 634
Score = 29.4 bits (66), Expect = 0.72
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 91 VDDLDIDAVVYNTLSTKFPEKMGVERITHHLLHGKI-LLEVEV 132
V+ LD + + N +T K+G+ER +LHGK EVEV
Sbjct: 188 VERLDKEGKLANYAATHDIGKLGIERYYEDVLHGKTGYEEVEV 230
>gnl|CDD|181493 PRK08593, PRK08593, 4-aminobutyrate aminotransferase;
Provisional.
Length = 445
Score = 28.5 bits (64), Expect = 1.0
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 16/51 (31%)
Query: 28 VDPFSSVSAAHGVGENVRHQIHKSHPEVSEV-------FIHIDPAYFQFSP 71
+D +S S+ +NV H + P V E FIH PAY P
Sbjct: 45 IDLLASASS-----QNVGH----APPRVVEAIKAQADKFIHYTPAYMYHEP 86
>gnl|CDD|234030 TIGR02834, spo_ytxC, putative sporulation protein YtxC. This
uncharacterized protein is part of a panel of proteins
conserved in all known endospore-forming Firmicutes
(low-GC Gram-positive bacteria), including
Carboxydothermus hydrogenoformans, and nowhere else
[Cellular processes, Sporulation and germination].
Length = 276
Score = 28.0 bits (63), Expect = 1.4
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 2/87 (2%)
Query: 42 ENVRHQIHKSHPEVSEVFIHIDPAYFQFSPSTMDQLGLEGCKAHSSNICVDDLDIDAVVY 101
+ +R+ + + V I +D F+ L E + L I+ ++
Sbjct: 180 KLLRYFVEIQDSRLEIVHIVVDGGSFRLYDENGRDLSSEELVELIDEVFESGLYIEDILI 239
Query: 102 NTLSTKFPEKMGVERITHHLLHGKILL 128
+ L + PEK ++ T H KI+L
Sbjct: 240 SPLISLAPEK--IKIHTDDPDHNKIIL 264
>gnl|CDD|182742 PRK10800, PRK10800, acyl-CoA thioesterase YbgC; Provisional.
Length = 130
Score = 26.2 bits (58), Expect = 4.2
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 92 DDLDIDAVVYNTLSTKFPEKMGVERITHHLLHGKILLEVEVS 133
+D D VVY+ F E+ E + HH + LL V+
Sbjct: 12 EDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALLAERVA 53
>gnl|CDD|99855 cd06101, citrate_synt, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) the carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) the nucleophilic attack of this
carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and form
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 265
Score = 26.5 bits (59), Expect = 4.4
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 78 GLEGCKAHSSNICVDDLDIDAVVYNTLSTK-FPEKMGVERITHHLLHGKI 126
GL G A S I V D D + Y + E E + + LL G++
Sbjct: 2 GLRGVAALESEISVIDGDEGGLRYRGYPIEELAENSSFEEVAYLLLTGEL 51
>gnl|CDD|204090 pfam08903, DUF1846, Domain of unknown function (DUF1846). This
family of proteins are functionally uncharacterized.
Some members of the family are annotated as
ATP-dependent peptidases. However, we can find no
support for this annotation.
Length = 490
Score = 26.9 bits (60), Expect = 4.5
Identities = 8/17 (47%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 74 MDQLG-LEGCKAHSSNI 89
+++L L+GC+AHS+ I
Sbjct: 445 LEKLPELKGCEAHSTVI 461
>gnl|CDD|184220 PRK13663, PRK13663, hypothetical protein; Provisional.
Length = 493
Score = 26.8 bits (60), Expect = 5.3
Identities = 11/17 (64%), Positives = 15/17 (88%), Gaps = 1/17 (5%)
Query: 74 MDQLG-LEGCKAHSSNI 89
M+QLG L+GC+AHS+ I
Sbjct: 447 MEQLGNLKGCEAHSTVI 463
>gnl|CDD|234118 TIGR03138, QueF, 7-cyano-7-deazaguanine reductase. This enzyme
catalyzes the 4-electron reduction of the cyano group of
7-cyano-7-deazaguanine (preQ0) to an amine. Although
related to a large family of GTP cyclohydrolases
(pfam01227), the relationship is structural and not
germane to the catalytic mechanism. This mode represents
the longer, gram-negative version of the enzyme as found
in E. coli. The enzymatic step represents the first
point at which the biosynthesis of queuosine in bacteria
and eukaryotes is distinguished from the biosynthesis of
archaeosine in archaea [Transcription, RNA processing].
Length = 275
Score = 26.1 bits (58), Expect = 6.1
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 84 AHSSNICVDDLDIDAVVY----NTLSTKFPEKMGVERITHHLL 122
A IC+DDLDI+ Y + L T ++ E + HLL
Sbjct: 136 AAPDGICIDDLDIEIDNYQPDPSLLKTDQSDEEVEETLYSHLL 178
>gnl|CDD|236986 PRK11792, queF, 7-cyano-7-deazaguanine reductase; Provisional.
Length = 273
Score = 25.9 bits (58), Expect = 7.2
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 69 FSPSTMDQLGLEGCKAHSSNICVDDLDIDAVVY 101
F + + A C+DDLDI+ Y
Sbjct: 124 FPLDEFEGQPI----AELPGECIDDLDIEIDNY 152
>gnl|CDD|235053 PRK02610, PRK02610, histidinol-phosphate aminotransferase;
Provisional.
Length = 374
Score = 26.2 bits (58), Expect = 7.4
Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 50 KSHPEVSEVFIHIDPAYFQFSPSTM 74
+S PE ++ + ID AYF+FS +T+
Sbjct: 194 RSLPE--DILVVIDEAYFEFSQTTL 216
>gnl|CDD|236332 PRK08668, PRK08668, NADH dehydrogenase subunit M; Validated.
Length = 610
Score = 26.1 bits (58), Expect = 8.2
Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 72 STMDQLGLEGCKAHSSNICVDD----LDIDAVVYNTLSTKFPEKMG 113
LG G H N + L AV+Y T +TK E MG
Sbjct: 316 GLGTSLGFAGGLFHVFNHALFKGLFFLIFAAVIYRTGTTKISE-MG 360
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is
unkown. The protein sequences are similar to the ArgK
protein in E. coli. ArgK protein is a membrane ATPase
which is required for transporting arginine, ornithine
and lysine into the cells by the arginine and ornithine
(AO system) and lysine, arginine and ornithine (LAO)
transport systems.
Length = 148
Score = 25.7 bits (57), Expect = 8.3
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 10 RLRGRRAGSSLYLDVHIVVDPFSSVSAAHGVGENVRHQIHKSHPEV 55
R RG+R + +DP S S +G+ +R + H S P V
Sbjct: 24 RARGKRVAV-------LAIDPSSPFSGGAILGDRIRMERHASDPGV 62
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
0.321 0.135 0.400
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,080,581
Number of extensions: 617302
Number of successful extensions: 520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 24
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.5 bits)