RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5526
(88 letters)
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 58.1 bits (141), Expect = 7e-13
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 10 ALSDGVVLCHLANHVRPRSVASIHVPSPAVPKLTMARCRRNVDNFLEACRKIGVEEGDLC 69
L DGV LC L N + P V V L+ + N++ L K+G + L
Sbjct: 25 DLKDGVALCALLNSLSPGLVDKKKVA----ASLSRFKKIENINLALSFAEKLGGKV-VLF 79
Query: 70 DRDSIVD 76
+ + +V+
Sbjct: 80 EPEDLVE 86
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 50.0 bits (120), Expect = 2e-09
Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 5 EELGPALSDGVVLCHLANHVRPRSVASIHVPSPAVPKLTMA-RCRRNVDNFLEACRKIGV 63
L DG+ LC L N + P + + N++ L K+GV
Sbjct: 23 NNFSTDLKDGIALCKLLNSLSPDLI------DKKKINPLSRFKRLENINLALNFAEKLGV 76
Query: 64 EE 65
Sbjct: 77 PV 78
>gnl|CDD|215849 pfam00307, CH, Calponin homology (CH) domain. The CH domain is
found in both cytoskeletal proteins and signal
transduction proteins. The CH domain is involved in
actin binding in some members of the family. However in
calponins there is evidence that the CH domain is not
involved in its actin binding activity. Most member
proteins have from two to four copies of the CH domain,
however some proteins such as calponin have only a
single copy.
Length = 104
Score = 43.0 bits (102), Expect = 6e-07
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 10 ALSDGVVLCHLANHVRPRSVASIHVPSPAVPKLTMARCRRNVDNFLEAC-RKIGV 63
L DG+ LC L N +RP + N++ LE +K+GV
Sbjct: 26 DLRDGLALCALLNKLRPGLI------DLKKVNKNRFDKLENLNLALEFAEKKLGV 74
>gnl|CDD|219007 pfam06395, CDC24, CDC24 Calponin. Is a calponin homology domain.
Length = 89
Score = 30.3 bits (69), Expect = 0.035
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 14 GVVLCHLANHVRPRSVASIHVPSPAVPKLTMARCRRNVDNFLEACRK 60
G LC L N ++P + V + + C+++V +FL AC+
Sbjct: 13 GYPLCALFNALQPEE--PLPVDTVSSDD--AKICKKSVYDFLLACKS 55
>gnl|CDD|227526 COG5199, SCP1, Calponin [Cytoskeleton].
Length = 178
Score = 30.3 bits (68), Expect = 0.065
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 2 SLPEELGPA------LSDGVVLCHLANHVRPRSVASIHVPSPAVPKLTMARCRRNVDNFL 55
L E+ P L DGV LC + N P I +P + M N+ +F+
Sbjct: 25 VLGEKFEPPGDLLSLLKDGVRLCRILNEASP---LDIKYKESKMPFVQM----ENISSFI 77
Query: 56 EACRKIGVEEGDL 68
+K+ V E +L
Sbjct: 78 NGLKKLRVPEYEL 90
>gnl|CDD|221350 pfam11971, CAMSAP_CH, CAMSAP CH domain. This domain is the
N-terminal CH domain from the CAMSAP proteins.
Length = 85
Score = 28.8 bits (65), Expect = 0.14
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 5 EELGPALSDGVVLCHLANHVRPRSV--ASIHVPSPAVPKLTMARCRRNVDNFLEACRK 60
E L SDG L L + P+ V I + +++A N+ E C +
Sbjct: 14 ENLTRDFSDGCALAALIHFYCPQLVPLHDICLK----ETMSVADSLYNIQLLQEFCEE 67
>gnl|CDD|213314 cd05967, PrpE, Propionyl-CoA synthetase (PrpE). PrpE catalyzes the
first step of the 2-methylcitric acid cycle for
propionate catabolism. It activates propionate to
propionyl-CoA in a two-step reaction, which proceeds
through a propionyl-AMP intermediate and requires ATP
and Mg2+. In Salmonella enterica, the PrpE protein is
required for growth of S. enterica on propionate and can
substitute for the acetyl-CoA synthetase (Acs) enzyme
during growth on acetate. PrpE can also activate
acetate, 3HP, and butyrate to their corresponding
CoA-thioesters, although with less efficiency.
Length = 607
Score = 28.4 bits (64), Expect = 0.40
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 17 LCHLA--NHV---RPRSVASIHVPSPAVP---KLTMARCRRNVDNFLEACRKIGVEEGDL 68
LC+ A H+ R +A I+ SP T A V RK+GV +GD
Sbjct: 42 LCYNAVDRHIEDGRGDQIALIYD-SPVTGTKRTYTYAELYDEVSRLAGVLRKLGVVKGDR 100
Query: 69 C 69
Sbjct: 101 V 101
>gnl|CDD|178740 PLN03199, PLN03199, delta6-acyl-lipid desaturase-like protein;
Provisional.
Length = 485
Score = 28.1 bits (62), Expect = 0.56
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 37 PAVPKLTMARCRRNVDNFLEACRKIGVE--EGDLCD 70
P +P+ +A+C V++F C++ GV+ E DL D
Sbjct: 426 PMLPRHNIAKCHALVESF---CKEWGVKYHEADLVD 458
>gnl|CDD|226679 COG4226, HicB, Predicted nuclease of the RNAse H fold, HicB
family [General function prediction only].
Length = 111
Score = 27.0 bits (60), Expect = 0.81
Identities = 6/14 (42%), Positives = 12/14 (85%)
Query: 51 VDNFLEACRKIGVE 64
+D++LE C++ G+E
Sbjct: 51 LDDYLEFCKERGIE 64
>gnl|CDD|233316 TIGR01217, ac_ac_CoA_syn, acetoacetyl-CoA synthase. This enzyme
catalyzes the first step of the mevalonate pathway of
IPP biosynthesis. Most bacteria do not use this pathway,
but rather the deoxyxylulose pathway [Central
intermediary metabolism, Other].
Length = 652
Score = 27.5 bits (61), Expect = 0.82
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 29 VASIHVPSPAVPKLTMARCRRNVDNFLEACRKIGVEEGD 67
V H P+P +T A RR V + A R +GV GD
Sbjct: 106 VDETHEPAP----VTWAELRRQVASLAAALRALGVRPGD 140
>gnl|CDD|233667 TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase. This model
represents the enzyme (UbiB) which catalyzes the first
hydroxylation step in the ubiquinone biosynthetic
pathway in bacteria. It is believed that the reaction is
2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This
model finds hits primarily in the proteobacteria. The
gene is also known as AarF in certain species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 437
Score = 26.9 bits (60), Expect = 1.5
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)
Query: 27 RSVASIHVPSPAVPKLTMARCRRNVDNFLEACRKIG 62
R VA +H + VP T ++ F +A R IG
Sbjct: 328 RRVAEVHFDAGYVPSDT------DMAEFEQAIRAIG 357
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 26.1 bits (58), Expect = 2.1
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 60 KIGVE--EGDLCDRDSIVDATQGSLSTLSNT 88
GVE EGDL D +S+V+A +G S T
Sbjct: 42 AAGVELVEGDLDDHESLVEALKGVDVVFSVT 72
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 26.5 bits (59), Expect = 2.1
Identities = 9/19 (47%), Positives = 9/19 (47%)
Query: 4 PEELGPALSDGVVLCHLAN 22
EE AL DGV L N
Sbjct: 711 REEYEEALEDGVEFKELLN 729
>gnl|CDD|233956 TIGR02630, xylose_isom_A, xylose isomerase. Members of this family
are the enzyme xylose isomerase (5.3.1.5), which
interconverts D-xylose and D-xylulose [Energy
metabolism, Sugars].
Length = 434
Score = 26.1 bits (58), Expect = 2.3
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 44 MARCRRNVDNFLEACRKIGVEEGDLC--DRD 72
M + + VD E K+GV C DRD
Sbjct: 73 MDKAKAKVDAAFEFFEKLGVPY--YCFHDRD 101
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 25.7 bits (57), Expect = 3.3
Identities = 21/64 (32%), Positives = 25/64 (39%), Gaps = 17/64 (26%)
Query: 5 EELGPALSDGVVLCHLANHVRPRSVASIHVPSP-AVPKLTMARCRRNVD---NFLEACRK 60
E + D VV HLA A + VP+ P NV N LEA RK
Sbjct: 24 EVVVIDRLDVVV--HLA--------ALVGVPASWDNPDEDF---ETNVVGTLNLLEAARK 70
Query: 61 IGVE 64
GV+
Sbjct: 71 AGVK 74
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 25.6 bits (56), Expect = 3.5
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 5/19 (26%)
Query: 51 VDNF-----LEACRKIGVE 64
VDNF +EACRK GV
Sbjct: 107 VDNFGTVNLVEACRKAGVT 125
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a
negative transcriptional regulator of various fungi,
involved in the post-translational modulation of the
GATA-type transcription factor AreA. NmrA lacks the
canonical GXXGXXG NAD-binding motif and has altered
residues at the catalytic triad, including a Met
instead of the critical Tyr residue. NmrA may bind
nucleotides but appears to lack any dehydrogenase
activity. HSCARG has been identified as a putative
NADP-sensing molecule, and redistributes and
restructures in response to NADPH/NADP ratios. Like
NmrA, it lacks most of the active site residues of the
SDR family, but has an NAD(P)-binding motif similar to
the extended SDR family, GXXGXXG. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical
SDRs are distinct from classical SDRs. Classical SDRs
have an TGXXX[AG]XG cofactor binding motif and a YXXXK
active site motif, with the Tyr residue of the active
site motif serving as a critical catalytic residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser and/or an Asn, contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. In addition to the Rossmann fold core
region typical of all SDRs, extended SDRs have a less
conserved C-terminal extension of approximately 100
amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 242
Score = 25.3 bits (56), Expect = 4.8
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 62 GVE--EGDLCDRDSIVDATQGSLSTLSNT 88
GVE +GDL D +S+ A +G T
Sbjct: 45 GVEVVQGDLDDPESLEAALKGVYGVFLVT 73
>gnl|CDD|147443 pfam05247, FlhD, Flagellar transcriptional activator (FlhD).
This family consists of several bacterial flagellar
transcriptional activator (FlhD) proteins. FlhD
combines with FlhC to form a regulatory complex in E.
coli, this complex has been shown to be a global
regulator involved in many cellular processes as well
as a flagellar transcriptional activator.
Length = 102
Score = 24.9 bits (55), Expect = 5.0
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 11 LSDGVVLCHLANHVRPRSVASIH 33
D +L L NH R ++ H
Sbjct: 69 FDDHALLSLLTNHSRDDALQQSH 91
>gnl|CDD|181219 PRK08068, PRK08068, transaminase; Reviewed.
Length = 389
Score = 25.3 bits (56), Expect = 5.0
Identities = 9/15 (60%), Positives = 11/15 (73%), Gaps = 2/15 (13%)
Query: 48 RRNVDNFLEACRKIG 62
RRN F+ ACR+IG
Sbjct: 302 RRNA--FISACREIG 314
>gnl|CDD|181779 PRK09326, PRK09326, F420H2 dehydrogenase subunit F; Provisional.
Length = 341
Score = 25.2 bits (55), Expect = 5.6
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 35 PSPA---VPKLTMARCRRNVDNFLEACRKIGVEEG 66
P P V KL + + N +++LE C K E G
Sbjct: 304 PKPGMELVKKLINMKHKNNAEHYLEVCEKFSFETG 338
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 24.7 bits (55), Expect = 6.9
Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 20 LANHVRPRS----VASIHVPSPAVPKLTMARC----RRNVDNFLEACRKIGV 63
LA V V I P +P + M + V+ F + GV
Sbjct: 67 LAAGVTLADVFELVREIREKDPTIPIVLMTYYNPIFQYGVERFAADAAEAGV 118
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid
dehydrogenase/isomerase family. The enzyme 3
beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase
(3 beta-HSD) catalyzes the oxidation and isomerisation
of 5-ene-3 beta-hydroxypregnene and
5-ene-hydroxyandrostene steroid precursors into the
corresponding 4-ene-ketosteroids necessary for the
formation of all classes of steroid hormones.
Length = 280
Score = 24.6 bits (54), Expect = 8.4
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 61 IGVEEGDLCDRDSIVDATQGS 81
I EGD+ D+ + A QGS
Sbjct: 47 ITYIEGDVTDKQDLRRALQGS 67
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 24.5 bits (53), Expect = 9.3
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 12/52 (23%)
Query: 16 VLCHLANHVRPRSVASIHVPSPAVPKLTMARCRRNVD---NFLEACRKIGVE 64
+ HLA + +S+ + + P + NVD N LEA R GV+
Sbjct: 67 AVIHLA------AQSSVPDSNASDPAEFL---DVNVDGTLNLLEAARAAGVK 109
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
0.318 0.133 0.395
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,290,882
Number of extensions: 334690
Number of successful extensions: 371
Number of sequences better than 10.0: 1
Number of HSP's gapped: 368
Number of HSP's successfully gapped: 33
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
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 (21.7 bits)
S2: 53 (24.2 bits)