RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15410
(87 letters)
>gnl|CDD|235691 PRK06074, PRK06074, NADH dehydrogenase subunit C; Provisional.
Length = 189
Score = 58.0 bits (141), Expect = 4e-12
Identities = 28/71 (39%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 16 LVDFGKYCAEILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGM 75
L + E LP I KV + G EL L + E ++ VL FL+D +F L+D+ G+
Sbjct: 4 LEELVAKLLEKLPDAIGKVTVAFG-ELTLKVPAEKILEVLTFLRDDPELRFEQLIDLTGV 62
Query: 76 DVPSRPNRFEV 86
D P R RFEV
Sbjct: 63 DYPERGKRFEV 73
>gnl|CDD|223921 COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD subunit
[Energy production and conversion].
Length = 176
Score = 42.3 bits (100), Expect = 3e-06
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 27 LPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86
L IE V + + EL L + P+ ++ VL+ LKD F L+D+ G+D P RFEV
Sbjct: 17 LSTVIETV-VVAEGELTLKVPPDELIDVLKALKDE---GFDHLLDLTGVDYPQETERFEV 72
>gnl|CDD|233657 TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, subunit C.
This model describes the C subunit of the NADH
dehydrogenase complex I in bacteria, as well as many
instances of the corresponding mitochondrial subunit
(NADH dehydrogenase subunit 9) and of the F420H2
dehydrogenase in Methanosarcina. Complex I contains
subunits designated A-N. This C subunit often occurs as
a fusion protein with the D subunit. This model
excludes the NAD(P)H and plastoquinone-dependent form
of chloroplasts and [Energy metabolism, Electron
transport].
Length = 121
Score = 37.6 bits (88), Expect = 1e-04
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 46 IIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFEV 86
I E ++ VL FLKD F L D++G+D P RFEV
Sbjct: 5 IKKEQLLEVLTFLKDPA-LGFELLTDVSGVDYPKE-KRFEV 43
>gnl|CDD|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase
subunit C/D; Provisional.
Length = 575
Score = 29.9 bits (68), Expect = 0.10
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 34 VQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNR 83
VQ T + + E ++ VL+FL+ +V L D+ G+D R +R
Sbjct: 16 VQATRTGIPVVWVKREQLLEVLRFLR-KLPKPYVMLFDLHGIDERLRTHR 64
>gnl|CDD|227188 COG4851, CamS, Protein involved in sex pheromone biosynthesis
[General function prediction only].
Length = 382
Score = 29.0 bits (65), Expect = 0.24
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 3 TIRKPIDEVARSHLVDFGKYCAEILPKYIEK-----VQITSGDELELLII 47
TI PI ++ +V F ++ + + +Y K V I SGD E LI+
Sbjct: 319 TIDIPIQYYGKAEIVAFTQFVTDRVEQYFPKNIDVQVNINSGDGQEALIV 368
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit
B/C/D; Provisional.
Length = 788
Score = 28.2 bits (63), Expect = 0.54
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 33 KVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNR 83
++ + D L PE V VL+ LK ++ F L D+A +D R +R
Sbjct: 237 RLDEGATDMLTYRCPPELVPEVLRHLKKRASSPFRRLEDLAAVDESCRRDR 287
>gnl|CDD|216981 pfam02338, OTU, OTU-like cysteine protease. This family is
comprised of a group of predicted cysteine proteases,
homologous to the Ovarian Tumour (OTU) gene in
Drosophila. Members include proteins from eukaryotes,
viruses and pathogenic bacterium. The conserved
cysteine and histidine, and possibly the aspartate,
represent the catalytic residues in this putative group
of proteases.
Length = 123
Score = 27.5 bits (61), Expect = 0.57
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 4 IRKPIDEVARSHLVDFGKYCAEILPKYIEKVQITS--GDELELLIIPE 49
+R+ + E R + DF K+ E +Y + + G +E+ +
Sbjct: 27 LREAVVEYLRENREDFEKFLEEDENEYYKWISKDGAWGGNIEIFALAH 74
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 27.5 bits (61), Expect = 0.89
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 8/38 (21%)
Query: 23 CAEIL-------PKYIEKVQITSGDELELLIIPEGVVP 53
CA IL PK EK++IT+ EL L I +G++P
Sbjct: 321 CAAILWKSAKAAPKAAEKLRITAQ-ELCRLQIADGIIP 357
>gnl|CDD|179361 PRK02048, PRK02048, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Provisional.
Length = 611
Score = 26.7 bits (59), Expect = 1.8
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 18/66 (27%)
Query: 17 VDFGKYCAEILPKYIEKVQITSG---------------DE---LELLIIPEGVVPVLQFL 58
V F A++ +Y EKV+I G DE E+ I + VP L
Sbjct: 91 VHFNPKVADVAAQYAEKVRINPGNYVDPGRTFKKLEYTDEEYAQEIQKIRDRFVPFLNIC 150
Query: 59 KDHHTA 64
K++HTA
Sbjct: 151 KENHTA 156
>gnl|CDD|215333 PLN02618, PLN02618, tryptophan synthase, beta chain.
Length = 410
Score = 26.3 bits (58), Expect = 2.3
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 50 GVVPVLQFLKDHHTAQFVSLVDIAGMDVPSRPNRFE 85
GV P FLKD A++ S+ D ++ R +R E
Sbjct: 324 GVGPEHSFLKDTGRAEYYSVTDEEALEAFQRLSRLE 359
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including
YchF, possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis
suggest that YchF may be part of a nucleoprotein
complex and may function as a GTP-dependent
translational factor.
Length = 274
Score = 25.5 bits (57), Expect = 3.2
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 9/35 (25%)
Query: 49 EGVVPV----LQFLKDHHTAQ-----FVSLVDIAG 74
G+VPV L L + + + VDIAG
Sbjct: 37 VGIVPVPDERLDKLAEIVKPKKIVPATIEFVDIAG 71
>gnl|CDD|198034 smart00966, SpoVT_AbrB, SpoVT / AbrB like domain. This domain is
found in AbrB from Bacillus subtilis. The product of
the abrB gene is an ambiactive repressor and activator
of the transcription of genes expressed during the
transition state between vegetative growth and the
onset of stationary phase and sporulation. AbrB is
thought to interact directly with the transcription
initiation regions of genes under its control. AbrB
contains a helix-turn-helix structure, but this domain
ends before the helix-turn-helix begins. The product of
the B. subtilis gene spoVT is another member of this
family and is also a transcriptional regulator.
DNA-binding activity in this AbrB homologue requires
hexamerisation. Another family member has been isolated
from the Sulfolobus solfataricus and has been
identified as a homologue of bacterial repressor-like
proteins. The Escherichia coli family member SohA or
Prl1F appears to be bifunctional and is able to
regulate its own expression as well as relieve the
export block imposed by high-level synthesis of
beta-galactosidase hybrid proteins.
Length = 45
Score = 24.0 bits (53), Expect = 4.1
Identities = 11/28 (39%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 26 ILPKYI-EKVQITSGDELELLIIPEGVV 52
+PK + EK+ I GDE+EL + +G++
Sbjct: 10 TIPKEVREKLGIKEGDEVELEVDGDGII 37
>gnl|CDD|143595 cd07571, ALP_N-acyl_transferase, Apolipoprotein N-acyl
transferase (class 9 nitrilases). ALP N-acyl
transferase (Lnt), is an essential membrane-bound
enzyme in gram-negative bacteria, which catalyzes the
N-acylation of apolipoproteins, the final step in
lipoprotein maturation. This is a reverse amidase (i.e.
condensation) reaction. This subgroup belongs to a
larger nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as
1-13), this subgroup corresponds to class 9.
Length = 270
Score = 25.3 bits (56), Expect = 4.7
Identities = 8/50 (16%), Positives = 20/50 (40%)
Query: 25 EILPKYIEKVQITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAG 74
L +Y++ + + ++ +L++ PE +P A+ G
Sbjct: 23 ATLDRYLDLTRELADEKPDLVVWPETALPFDLQRDPDALARLARAARAVG 72
>gnl|CDD|166458 PLN02817, PLN02817, glutathione dehydrogenase (ascorbate).
Length = 265
Score = 25.0 bits (54), Expect = 5.7
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 27 LPKYIEKVQITSGDELELLIIPEGVVPVLQF 57
LP ++ V +T+ E L I PEG VPV++
Sbjct: 88 LPYDMKLVDLTNKPEWFLKISPEGKVPVVKL 118
>gnl|CDD|107286 cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like
transcription regulator from a novel metal-reducing
bacterium Alkaliphilus Metalliredigens (strain Qymf) and
its close homologs. This group includes the ligand
binding domain of the lacI-like transcription regulator
from a novel metal-reducing bacterium Alkaliphilus
Metalliredigens (strain Qymf) and its close homologs.
Qymf is a strict anaerobe that could be grown in the
presence of borax and its cells are straight rods that
produce endospores. This group is a member of the
LacI-GalR family repressors that are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 265
Score = 24.8 bits (55), Expect = 7.4
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 8/33 (24%)
Query: 1 MTTIRKPIDEVARSHLVDFGKYCAEILPKYIEK 33
+TTIR+PI+E+A++ ++L K IE
Sbjct: 221 LTTIRQPIEEIAKT--------AVDLLIKQIEG 245
>gnl|CDD|212586 cd11717, THUMP_THUMPD1_like, THUMP domain-containing protein
1-like. This family contains THUMP domain-only
proteins including THUMP domain-containing protein 1
and Saccharomyces cerevisiae Tan1. Tan1 is non
essential and has been shown to be required for the
formation of the modified nucleoside
N(4)-acetylcytidine (ac(4)C) in tRNA. To date, there is
no functional information available about THUMPD1. The
THUMP domain is named after thiouridine synthases,
methylases and PSUSs. The domain consists of about 110
amino acid residues. It is predicted to be an
RNA-binding domain and probably functions by delivering
a variety of RNA modification enzymes to their targets.
Length = 158
Score = 24.5 bits (54), Expect = 7.6
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 7 PIDEVARSHLVDFGKYCAEILPKYIEKVQ 35
PID ++ L + K E+L K+ +
Sbjct: 70 PIDVTCKASLEEIEKLAKELLKKHFPTAE 98
>gnl|CDD|192187 pfam08964, DUF1881, Protein of unkown function (DUF1881). This
domain is found in a set of hypothetical bacterial and
eukaryotic proteins, as well as in various
calcium-dependent cell adhesion molecules.
Length = 200
Score = 24.7 bits (54), Expect = 7.8
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 18 DFGKYCAEILPKYIEKVQITSGDELELLI---IPEGVVPVLQ-FLKDHHT 63
D GKY ++P + V+I SGD+++ I P V ++D HT
Sbjct: 102 DDGKYSMTVIPYQVNPVEIVSGDDVQYPIVGLNPPDSEIVTAIAIRDTHT 151
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 24.7 bits (54), Expect = 8.7
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 2 TTIRKPIDEVARSHLVDFGKYCAEILPKYIEKVQITS------GDELELLI 46
I+K ++ + HL ++ +Y + P + K S DEL L
Sbjct: 555 AEIKKEFVDLIKKHLSNWEEYYKGLFPHKVNKYVFDSLYEEGKFDELNSLF 605
>gnl|CDD|239875 cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B
(NDPk7B): The nm23-H7 class of nucleoside diphosphate
kinase (NDPk7) consists of an N-terminal DM10 domain
and two functional catalytic NDPk modules, NDPk7A and
NDPk7B. The function of the DM10 domain, which also
occurs in multiple copies in other proteins, is
unknown. NDPk7 is predominantly expressed in testes,
although appreciable amount are also found in liver,
heart, brain, ovary, small intestine and spleen. The
nm23-H7 gene is located in or near the hereditary
prostrate cancer susceptibility locus. Nm23-H7 may be
involved in the development of colon and gastric
carcinoma, the latter possibly in a type-specific
manner.
Length = 134
Score = 24.1 bits (53), Expect = 9.3
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 36 ITSGDELELLIIPEGVVPVLQFLKDHHTAQFVSLVDIAGMDVPSR 80
+T + E L + +GVVP L + D T+ ++IAG +
Sbjct: 39 LTRANAEEFLEVYKGVVPELPAMVDELTSGPCIALEIAGENAVKT 83
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
0.322 0.141 0.410
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,606,464
Number of extensions: 383943
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 25
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (21.9 bits)
S2: 53 (24.0 bits)