RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12141
(142 letters)
>gnl|CDD|202009 pfam01849, NAC, NAC domain.
Length = 50
Score = 68.3 bits (168), Expect = 1e-16
Identities = 21/50 (42%), Positives = 33/50 (66%)
Query: 56 KKLAVNTIPGIEEVNMIKEDGTIIHFNNPKAQASLAANTFAITGHGETRE 105
KKL + I G+EEV + K+DG ++ FNNPK Q S +NT+ + G + ++
Sbjct: 1 KKLGLKPIEGVEEVTIRKKDGKVLVFNNPKVQKSPGSNTYVVFGEAKEKD 50
>gnl|CDD|240623 cd05199, SDH_like, Saccharopine Dehydrogenase like proteins.
Saccharopine Dehydrogenase (SDH) and related proteins,
including bifunctional lysine ketoglutarate
reductase/SDH enzymes and N(5)-(carboxyethyl)ornithine
synthases. SDH catalyzes the final step in the
reversible NAD-dependent oxidative deamination of
saccharopine to alpha-ketoglutarate and lysine, in the
alpha-aminoadipate pathway of L-lysine biosynthesis.
SDH is structurally related to formate dehydrogenase
and similar enzymes, having a 2-domain structure in
which a Rossmann-fold NAD(P)-binding domain is inserted
within the linear sequence of a catalytic domain of
related structure. Bifunctional lysine ketoglutarate
reductase/SDH protein is a pair of enzymes linked on a
single polypeptide chain that catalyze the initial,
consecutive steps of lysine degradation. These proteins
are related to the 2-domain saccharopine
dehydrogenases.
Length = 319
Score = 32.6 bits (75), Expect = 0.046
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 2 NKGDKRVVMNPELLKRLQQQAGQVRI 27
D+RV + PE K LQ + V I
Sbjct: 10 TPPDRRVPLTPEQCKELQAKYPGVEI 35
>gnl|CDD|215265 PLN02478, PLN02478, alternative oxidase.
Length = 328
Score = 28.3 bits (63), Expect = 1.2
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 22 AGQVRIGGKGTPRRKKKVVHTTA---ATDDKKLQSSLKK--LAVNTIPGIEEVNMIKEDG 76
G RIG K KK + AT++K S++K A+ + GIE + KEDG
Sbjct: 35 FGGFRIGSKHAQEEKKLAEEEESSGKATENKDEGSTVKGGQKAIVSYWGIEPAKITKEDG 94
Query: 77 T 77
T
Sbjct: 95 T 95
>gnl|CDD|225293 COG2445, COG2445, Uncharacterized conserved protein [Function
unknown].
Length = 138
Score = 27.3 bits (61), Expect = 2.2
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 36 KKKVVHTTAATDDKKLQSSLKKLAVNTIPGIEEVNMIKE 74
+ +VH A D +K+ SLK+L + +EE+ + E
Sbjct: 95 RNILVHRYWAVDPEKVYRSLKELLEDYENFLEEIRKLLE 133
>gnl|CDD|223686 COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP
family) [General function prediction only].
Length = 258
Score = 27.4 bits (61), Expect = 2.7
Identities = 20/93 (21%), Positives = 30/93 (32%), Gaps = 11/93 (11%)
Query: 42 TTAATDDKKLQSSLKKLAVNTIPGIEEVNMIKEDGTIIHFNNPKAQASLAANTFAITGHG 101
T + + + L+ L + IPGIE G IIH + +
Sbjct: 41 TVRGLLEARRAAGLR-LGITVIPGIEI--STTWGGHIIHILGLGIDITDEPLVEGLARQQ 97
Query: 102 ETRE-----ITEMLPGILSQLGPEGLTQLKRLA 129
RE I E L + P ++LA
Sbjct: 98 LYREERLEEIKERLGKA---IIPHPFEGARKLA 127
>gnl|CDD|100016 cd02187, beta_tubulin, The tubulin superfamily includes five
distinct families, the alpha-, beta-, gamma-, delta-,
and epsilon-tubulins and a sixth family (zeta-tubulin)
which is present only in kinetoplastid protozoa. The
alpha- and beta-tubulins are the major components of
microtubules, while gamma-tubulin plays a major role in
the nucleation of microtubule assembly. The delta- and
epsilon-tubulins are widespread but unlike the alpha,
beta, and gamma-tubulins they are not ubiquitous among
eukaryotes. The alpha/beta-tubulin heterodimer is the
structural subunit of microtubules. The alpha- and
beta-tubulins share 40% amino-acid sequence identity,
exist in several isotype forms, and undergo a variety of
posttranslational modifications. The structures of
alpha- and beta-tubulin are basically identical: each
monomer is formed by a core of two beta-sheets
surrounded by alpha-helices. The monomer structure is
very compact, but can be divided into three regions
based on function: the amino-terminal nucleotide-binding
region, an intermediate taxol-binding region and the
carboxy-terminal region which probably constitutes the
binding surface for motor proteins.
Length = 425
Score = 27.2 bits (61), Expect = 3.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 50 KLQSSLKKLAVNTIP 64
+L S L+KLAVN +P
Sbjct: 244 QLNSDLRKLAVNMVP 258
>gnl|CDD|217609 pfam03548, LolA, Outer membrane lipoprotein carrier protein LolA.
Length = 165
Score = 26.5 bits (59), Expect = 3.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 66 IEEVNMIKEDG--TIIHFNNPKAQASLAANTFAIT 98
+ + +I +DG T I F+N K +LA + F T
Sbjct: 131 LRQFTVIDQDGQRTTITFSNVKTNPTLADDLFKFT 165
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 27.2 bits (60), Expect = 3.9
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 11/69 (15%)
Query: 69 VNMIKEDGTIIHFNNPKAQASLAANTFAITGHGETREITEMLP-GILSQLGPEGLTQLKR 127
+++I+ DGT++HFN K A+L A T +I M P +L ++ LTQ
Sbjct: 118 LSVIRRDGTVVHFNPMKISAALEKAFRA------TDKIEGMTPSSVLEEI--NALTQ--N 167
Query: 128 LATSVAGMC 136
+ + C
Sbjct: 168 IVEEILECC 176
>gnl|CDD|225826 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
production and conversion].
Length = 356
Score = 27.0 bits (60), Expect = 4.4
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 7/87 (8%)
Query: 3 KGDKRVVMNPELLKRLQQQAGQVRI-GGKGT----PRRKKKVVHTTAATDDKKLQSSLKK 57
+ RV PE +K+L + V + G G P T D Q+ +
Sbjct: 10 ANETRVAATPETVKKLVKLGFDVVVESGAGLRASFPDAAYVAAGATIGAADAVWQADI-- 67
Query: 58 LAVNTIPGIEEVNMIKEDGTIIHFNNP 84
+ P E+ ++KE T++ F NP
Sbjct: 68 ILKVRAPSAAEIALLKEGATLVSFLNP 94
>gnl|CDD|239188 cd02787, MopB_CT_ydeP, The MopB_CT_ydeP CD includes a group of
related uncharacterized bacterial molybdopterin-binding
oxidoreductase-like domains with a putative
molybdopterin cofactor binding site. This CD is of the
conserved molybdopterin_binding C-terminal (MopB_CT)
region present in many, but not all, MopB homologs.
Length = 112
Score = 26.1 bits (58), Expect = 4.6
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 4 GDKRVV-MNPELLKRLQQQAGQ----VRIGGKGTPRR 35
G + VV MNP+ + RL +AG G G R
Sbjct: 28 GRRDVVFMNPDDIARLGLKAGDRVDLESAFGDGQGRI 64
>gnl|CDD|181915 PRK09504, sufA, iron-sulfur cluster assembly scaffold protein;
Provisional.
Length = 122
Score = 25.9 bits (57), Expect = 5.0
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 45 ATDDKKLQSSLKKLAV--NTIPGIE--EVNMIKED-GTIIHFNNPKAQ 87
DD + KL V +P I+ EV+ ++E I F+NPKAQ
Sbjct: 64 DKDDLVFEHDGAKLFVPLQAMPFIDGTEVDYVREGLNQIFKFHNPKAQ 111
>gnl|CDD|132248 TIGR03204, pimC_large, pimeloyl-CoA dehydrogenase, large subunit.
Members of this protein family are the PimC proteins of
species such as Rhodopseudomonas palustris and
Bradyrhizobium japonicum. The pimFABCDE operon encodes
proteins for the metabolism of straight chain
dicarboxylates of seven to fourteen carbons. Especially
relevant is pimeloyl-CoA, basis of the gene symbol, as
it is a catabolite of benzoyl-CoA degradation, which
occurs in Rhodopseudomonas palustris.
Length = 395
Score = 26.5 bits (58), Expect = 5.2
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 4 GDKRVVMNPELLKRLQQQAGQVRIGGK 30
G RV ++ E ++R++ A +V GGK
Sbjct: 246 GIARVGVSKERIRRIKDLAAKVESGGK 272
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 26.4 bits (59), Expect = 6.3
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 9/45 (20%)
Query: 80 HFNNPKAQASLAANTFAITG-HGETREITEMLPGILSQLGPEGLT 123
H N+P+AQ LA A++ G T E+T I P T
Sbjct: 566 HLNSPRAQQRLAE---ALSELLGRTVELT-----IEEDDNPAVET 602
>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate
binding domain of LysR-type transcriptional regulators
that are involved in the catabolism of dinitrotoluene,
naphthalene and gamma-hexachlorohexane; contains the
type 2 periplasmic binding fold. This CD includes
LysR-like bacterial transcriptional regulators, DntR,
NahR, and LinR, which are involved in the degradation
of aromatic compounds. The transcription of the genes
encoding enzymes involved in such degradation is
regulated and expression of these enzymes is enhanced
by inducers, which are either an intermediate in the
metabolic pathway or compounds to be degraded. DntR
from Burkholderia species controls genes encoding
enzymes for oxidative degradation of the nitro-aromatic
compound 2,4-dinitrotoluene. The active form of DntR is
homotetrameric, consisting of a dimer of dimers. NahR
is a salicylate-dependent transcription activator of
the nah and sal operons for naphthalene degradation.
Salicylic acid is an intermediate of the oxidative
degradation of the aromatic ring in soil bacteria.
LinR positively regulates expression of the genes (linD
and linE) encoding enzymes for
gamma-hexachlorocyclohexane (a haloorganic insecticide)
degradation. Expression of linD and linE are induced by
their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ)
and chlorohydroquinone (CHQ). The structural topology
of this substrate-binding domain is most similar to
that of the type 2 periplasmic binding proteins (PBP2),
which are responsible for the uptake of a variety of
substrates such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 201
Score = 26.0 bits (58), Expect = 6.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 8 VVMNPELLKRLQQQAGQVRI 27
+ P LL L++ A VRI
Sbjct: 12 MYFLPRLLAALREVAPGVRI 31
>gnl|CDD|131052 TIGR01997, sufA_proteo, FeS assembly scaffold SufA. This model
represents the SufA protein of the SUF system of
iron-sulfur cluster biosynthesis. This system performs
FeS biosynthesis even during oxidative stress and tends
to be absent in obligate anaerobic and microaerophilic
bacteria [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 107
Score = 25.6 bits (56), Expect = 6.9
Identities = 6/21 (28%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 68 EVNMIKED-GTIIHFNNPKAQ 87
+V+ ++ FNNP A
Sbjct: 76 QVDFVRTTLRQGFKFNNPNAT 96
>gnl|CDD|178807 PRK00031, lolA, lipoprotein chaperone; Reviewed.
Length = 195
Score = 25.7 bits (57), Expect = 7.9
Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 49 KKLQSSLKKLAVNTIPG-IEEVNMIKEDG--TIIHFNNPKAQASLAANTF 95
K ++ K+ + G + +++ +DG T+I F+N + +L A+ F
Sbjct: 133 KAKDTNFKQFTIGFRNGTLASFSLVDQDGQRTLITFSNIQKNPALDADKF 182
>gnl|CDD|237388 PRK13443, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 136
Score = 25.7 bits (56), Expect = 8.2
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 96 AITGHGETREITEMLPGILSQLGPEGLTQ 124
A+ GH T IT + PGIL GP G +
Sbjct: 35 AMEGHAPT--ITTLRPGILRAHGPSGTQE 61
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
0.314 0.131 0.358
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,075,027
Number of extensions: 629780
Number of successful extensions: 590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 33
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.6 bits)