RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2138
(208 letters)
>gnl|CDD|214648 smart00401, ZnF_GATA, zinc finger binding to DNA consensus
sequence [AT]GATA[AG].
Length = 52
Score = 35.9 bits (83), Expect = 0.001
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 36 SNKPCESCNVTVSTNWFPWYSGTK-ICINCHAFWRKYGGLKIP 77
S + C +C T + W SG K +C C +++K+GGLK P
Sbjct: 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRP 44
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.5 bits (81), Expect = 0.013
Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 11/100 (11%)
Query: 76 IPGKLSDGELDYL--KPNKKSGSSSLSEED---RIGPSG----LVGHRPHRCSVPGCSKE 126
I G +S GE+ + P S S+ I + +P++C V GC+K+
Sbjct: 301 IRGGISTGEMIDVRKLPCTNSSSNGKLAHGGERNIDTPSRMLKVKDGKPYKCPVEGCNKK 360
Query: 127 FKLKAHLHRHLATGHGLVARPGSPRPIMKTRNAFYLRATP 166
+K + L H+ GH +P P N F + P
Sbjct: 361 YKNQNGLKYHMLHGHQNQKLHENPSPE--KMNIFSAKDKP 398
>gnl|CDD|238123 cd00202, ZnF_GATA, Zinc finger DNA binding domain; binds
specifically to DNA consensus sequence [AT]GATA[AG]
promoter elements; a subset of family members may also
bind protein; zinc-finger consensus topology is
C-X(2)-C-X(17)-C-X(2)-C.
Length = 54
Score = 30.8 bits (70), Expect = 0.052
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 39 PCESCNVTVSTNWFPWYSGTK-ICINCHAFWRKYG 72
C +C T + W SG +C C +W+K+G
Sbjct: 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35
>gnl|CDD|235073 PRK02813, PRK02813, putative aminopeptidase 2; Provisional.
Length = 428
Score = 30.2 bits (69), Expect = 0.66
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 3 EAEVDMAEYNPHDLFFHDVGPGMVNGANGDVLISN 37
E VD + DLF +D PG + GANG+ IS+
Sbjct: 197 ELGVDADDILDFDLFLYDTQPGALIGANGE-FISS 230
>gnl|CDD|215745 pfam00141, peroxidase, Peroxidase.
Length = 180
Score = 29.5 bits (67), Expect = 0.83
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 16 LFFHDVGPGMVNGANGDVLISNKP 39
L FHD V G +G VL+ +P
Sbjct: 22 LHFHDCF---VGGCDGSVLLDFEP 42
>gnl|CDD|109380 pfam00320, GATA, GATA zinc finger. This domain uses four
cysteine residues to coordinate a zinc ion. This domain
binds to DNA. Two GATA zinc fingers are found in the
GATA transcription factors. However there are several
proteins which only contains a single copy of the
domain.
Length = 36
Score = 27.2 bits (61), Expect = 0.85
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 40 CESCNVTVSTNWFPWYSGTK-ICINCHAFWRKYG 72
C +C T + W G + +C C ++RK+G
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGLYYRKHG 34
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) 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. Extended SDRs have additional
elements in the C-terminal region, 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 KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 448
Score = 29.2 bits (66), Expect = 1.5
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 5/25 (20%)
Query: 129 LKAHLHRHLATGHG-----LVARPG 148
L A L RHL T HG LV+R G
Sbjct: 205 LGALLARHLVTEHGVRHLLLVSRRG 229
>gnl|CDD|172457 PRK13951, PRK13951, bifunctional shikimate kinase/3-dehydroquinate
synthase; Provisional.
Length = 488
Score = 29.1 bits (65), Expect = 1.9
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 137 LATGHGLVARPGSPRPIMKTRNAFYLRATP 166
+ATG G+V P + R ++K +L A P
Sbjct: 74 VATGGGVVIDPEN-RELLKKEKTLFLYAPP 102
>gnl|CDD|234237 TIGR03507, decahem_SO1788, decaheme c-type cytochrome, OmcA/MtrC
family. The protein SO_1778 (MtrC) of Shewanella
oneidensis MR-1, and its paralog SO_1779 (OmcA), with
which it intteracts, are large decaheme proteins, about
900 amino acids in length, involved in the use of
manganese [Mn(III/IV)] and iron [Fe(III)] as terminal
electron acceptors. This model represents these and
similar decaheme proteins, found also in Rhodoferax
ferrireducens DSM 15236, Aeromonas hydrophila ATCC7966,
and a few other bacterial species [Energy metabolism,
Electron transport].
Length = 659
Score = 28.6 bits (64), Expect = 2.5
Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 8/55 (14%)
Query: 19 HDVGPGMVNGA-NGDVLISNKPCESCNVTVSTNW------FPWYSGTKICINCHA 66
H A N + S C SC+ V+ T+ C CH
Sbjct: 247 HSGANTKTADADNWKTVPSMAACGSCHDNVNFATGANHVNQTQADDTQ-CAACHN 300
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 28.5 bits (63), Expect = 3.0
Identities = 13/58 (22%), Positives = 17/58 (29%)
Query: 90 PNKKSGSSSLSEEDRIGPSGLVGHRPHRCSVPGCSKEFKLKAHLHRHLATGHGLVARP 147
S SS L+ R +P C C K F L RH+ +
Sbjct: 296 NISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353
>gnl|CDD|218591 pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein.
This family consists of several ROS/MUCR transcriptional
regulator proteins. The ros chromosomal gene is present
in octopine and nopaline strains of Agrobacterium
tumefaciens as well as in Rhizobium meliloti. This gene
encodes a 15.5-kDa protein that specifically represses
the virC and virD operons in the virulence region of the
Ti plasmid and is necessary for succinoglycan
production. Sinorhizobium meliloti can produce two types
of acidic exopolysaccharides, succinoglycan and
galactoglucan, that are interchangeable for infection of
alfalfa nodules. MucR from Sinorhizobium meliloti acts
as a transcriptional repressor that blocks the
expression of the exp genes responsible for
galactoglucan production therefore allowing the
exclusive production of succinoglycan.
Length = 130
Score = 27.1 bits (61), Expect = 3.8
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 123 CSKEFK-LKAHLHRHLATGHGL 143
K+FK LK RHL T HGL
Sbjct: 76 DGKKFKTLK----RHLRTHHGL 93
>gnl|CDD|224281 COG1362, LAP4, Aspartyl aminopeptidase [Amino acid transport and
metabolism].
Length = 437
Score = 27.7 bits (62), Expect = 4.6
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 3 EAEVDMAEYNPHDLFFHDVGPGMVNGANGDVLIS 36
+ V+ ++ DL D + GA+G+ L +
Sbjct: 204 QLGVEEEDFVSFDLILVDAQKARLVGADGEFLSA 237
>gnl|CDD|184072 PRK13475, PRK13475, ribulose bisphosphate carboxylase; Provisional.
Length = 443
Score = 27.0 bits (60), Expect = 8.5
Identities = 11/19 (57%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 133 LHRHLATGHGLVARPGSPR 151
LH H A GHG V P S R
Sbjct: 284 LHYHRA-GHGAVTSPSSKR 301
>gnl|CDD|227651 COG5347, COG5347, GTPase-activating protein that regulates ARFs
(ADP-ribosylation factors), involved in ARF-mediated
vesicular transport [Intracellular trafficking and
secretion].
Length = 319
Score = 26.7 bits (59), Expect = 9.2
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 36 SNKPCESCNVTVSTNWFPWYSGTKICINCHAFWRKYG 72
SNK C C + W G +CI+C R G
Sbjct: 19 SNKKCADCG-APNPTWASVNLGVFLCIDCAGVHRSLG 54
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 0.138 0.455
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,525,994
Number of extensions: 936398
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 688
Number of HSP's successfully gapped: 19
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
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: 57 (25.8 bits)