RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15123
(278 letters)
>gnl|CDD|219000 pfam06367, Drf_FH3, Diaphanous FH3 Domain. This region is found in
the Formin-like and and diaphanous proteins.
Length = 197
Score = 130 bits (330), Expect = 2e-37
Identities = 57/124 (45%), Positives = 83/124 (66%)
Query: 116 YDLLDALEKDASEDVSVQLKVFIEHKEEDYYEFIQRFDNVRMEIDDVNDCFETVRNMVMD 175
+LD L + +E + QL++F E++EED E ++RFD+V +++DD + FE ++N V D
Sbjct: 74 DRILDKLRELENEKLDDQLQIFEENREEDVEELLERFDDVNVDLDDPVELFELLKNKVKD 133
Query: 176 SACEPYLLSILQHLLFIRDDQYVRLAYYKLLEECVSQIVLHRGGCDPDFRSSRRFQLDVQ 235
+ EP+ LSILQHLL IRDD+ Y+KLLEE VSQIVLHR DPDF + +D+
Sbjct: 134 TEAEPHFLSILQHLLLIRDDEEELPQYWKLLEELVSQIVLHRTKPDPDFDERKNLNIDIN 193
Query: 236 PLVE 239
L++
Sbjct: 194 RLLD 197
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 38.5 bits (89), Expect = 0.004
Identities = 17/78 (21%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 96 PKGTWPLDQTRPADSINRINYDLLDALEKDASEDVSVQLKVFIEHKEEDYYEFIQRFDNV 155
PKG+W L ++ D + + + ++ ++ +V++ +V++ E Y+E F+N+
Sbjct: 395 PKGSWELKKSWKLDKVYDVTEKVRKSVYEEPDREVTMASRVWVGGGGEGYFEVELTFENM 454
Query: 156 RMEIDDVND---CFETVR 170
++E V + C++ V+
Sbjct: 455 KLEDKHVQEPAGCYDAVQ 472
>gnl|CDD|173832 cd00684, Terpene_cyclase_plant_C1, Plant Terpene Cyclases, Class 1.
This CD includes a diverse group of monomeric plant
terpene cyclases (Tspa-Tspf) that convert the acyclic
isoprenoid diphosphates, geranyl diphosphate (GPP),
farnesyl diphosphate (FPP), or geranylgeranyl
diphosphate (GGPP) into cyclic monoterpenes, diterpenes,
or sesquiterpenes, respectively; a few form acyclic
species. Terpnoid cyclases are soluble enzymes localized
to the cytosol (sesquiterpene synthases) or plastids
(mono- and diterpene synthases). All monoterpene and
diterpene synthases have restrict substrate specificity,
however, some sesquiterpene synthases can accept both
FPP and GPP. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
diphosphates, via bridging Mg2+ ions (K+ preferred by
gymnosperm cyclases), inducing conformational changes
such that an N-terminal region forms a cap over the
catalytic core. Loss of diphosphate from the
enzyme-bound substrate (GPP, FPP, or GGPP) results in an
allylic carbocation that electrophilically attacks a
double bond further down the terpene chain to effect the
first ring closure. Unlike monoterpene, sesquiterene,
and macrocyclic diterpenes synthases, which undergo
substrate ionization by diphosphate ester scission,
Tpsc-like diterpene synthases catalyze cyclization
reactions by an initial protonation step producing a
copalyl diphosphate intermediate. These enzymes lack the
aspartate-rich sequences mentioned above. Most diterpene
synthases have an N-terminal, internal element (approx
210 aa) whose function is unknown.
Length = 542
Score = 29.1 bits (66), Expect = 2.8
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 146 YEFIQRFD----NVRMEIDDVNDCFETVRNMVMDSACEPYLLSILQHLLFIRDDQYVRL- 200
+ +++ + E VR M+ DS Y + + + L I D+ RL
Sbjct: 13 DDHFLSLSSDYSEEDELEEEIEELKEEVRKMLEDS---EYPVDLFERLWLI--DRLQRLG 67
Query: 201 -AYY--KLLEECVSQI 213
+Y+ ++E + I
Sbjct: 68 ISYHFEDEIKEILDYI 83
>gnl|CDD|218517 pfam05236, TAF4, Transcription initiation factor TFIID component
TAF4 family. This region of similarity is found in
Transcription initiation factor TFIID component TAF4.
Length = 255
Score = 28.5 bits (64), Expect = 3.2
Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 22/81 (27%)
Query: 174 MDSACEPYLLSILQHLLFIRDDQYVRLAYYKLLEECVSQIVLHRGGCDPDFRSSRRFQLD 233
+ ACE L +IL L+ + R K D R D
Sbjct: 73 ISHACEERLRNILTKLIVLSRH---RRDGIKS-----------------DPNYEIR--SD 110
Query: 234 VQPLVEHLAEKSKTEEDRRVE 254
V+ + LA+K K EE+RRVE
Sbjct: 111 VRRQLRFLAQKQKEEEERRVE 131
>gnl|CDD|239034 cd02117, NifH_like, This family contains the NifH (iron protein) of
nitrogenase, L subunit (BchL/ChlL) of the
protochlorophyllide reductase and the BchX subunit of
the Chlorophyllide reductase. Members of this family use
energey from ATP hydrolysis and transfer electrons
through a Fe4-S4 cluster to other subunit for reduction
of substrate.
Length = 212
Score = 28.3 bits (64), Expect = 3.8
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 219 GCDPDFRSSRR-FQLDVQPLVEHLAEKSKTEEDRRVEDL 256
GCDP S+R + LA + ED +ED+
Sbjct: 35 GCDPKADSTRLLLGGKAPTTILELAAEDGHVEDLELEDV 73
>gnl|CDD|189018 cd09839, M1_TAF2, TATA binding protein (TBP) associated factor 2.
This family includes TATA binding protein (TBP)
associated factor 2 (TAF2, TBP-associated factor
TAFII150, transcription initiation factor TFIID subunit
2, RNA polymerase II TBP-associated factor subunit B),
and has homology to the aminopeptidase N (APN)
subfamily, belonging to the M1 gluzincin family. TAF2 is
part of the TFIID multidomain subunit complex essential
for transcription of most protein-encoded genes by RNA
polymerase II. TAF2 is known to interact with the
initiator element (Inr) found at the transcription start
site of many genes, thus possibly playing a key role in
promoter binding as well as start-site selection. Image
analysis has shown TAF2 to form a complex with TAF1 and
TBP, inferring its role in promoter recognition.
Peptidases in the M1 family bind a single catalytic zinc
ion which is tetrahedrally co-ordinated by three amino
acid ligands and a water molecule that forms the
nucleophile on activation during catalysis. TAF2,
however, does not seem to contain any of the active site
residues.
Length = 507
Score = 28.5 bits (64), Expect = 3.9
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 16/79 (20%)
Query: 32 PCGLERDDVSDFCSLAQYYD----------------YKTPRSFKTVTLADPEDEDGEIEV 75
C + +V+ + Y D + + S V+ D + +GE+ +
Sbjct: 42 QCRILSVEVNGEPAKFTYNDPTQELCRDEPWKSVLQHASDASLSAVSYVDLDANNGELLI 101
Query: 76 DRCKYDMKKIIEFPGFNVR 94
K K + E VR
Sbjct: 102 SVPKEVRKLVDEQKVLRVR 120
>gnl|CDD|132143 TIGR03099, dCO2ase_PEP1, pyridoxal-dependent decarboxylase,
exosortase A system-associated. The sequences in this
family contain the pyridoxal binding domain (pfam02784)
and C-terminal sheet domain (pfam00278) of a family of
Pyridoxal-dependent decarboxylases. Characterized
enzymes in this family decarboxylate substrates such as
ornithine, diaminopimelate and arginine. The genes of
the family modeled here, with the exception of those
observed in certain Burkholderia species, are all found
in the context of exopolysaccharide biosynthesis loci
containing the exosortase/PEP-CTERM protein sorting
system. More specifically, these are characteristic of
the type 1 exosortase system represented by the Genome
Property GenProp0652. The substrate of these enzymes may
be a precursor of the carrier or linker which is
hypothesized to release the PEP-CTERM protein from the
exosortase enzyme. These enzymes are apparently most
closely related to the diaminopimelate decarboxylase
modeled by TIGR01048 which may suggest a similarity (or
identity) of substrate.
Length = 398
Score = 27.8 bits (62), Expect = 6.4
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 252 RVEDLSAFLFKYGLEFPSFHIFP 274
+V AF+ L+F FHIF
Sbjct: 172 QVPAALAFIKAADLDFQGFHIFA 194
>gnl|CDD|178182 PLN02569, PLN02569, threonine synthase.
Length = 484
Score = 27.9 bits (62), Expect = 6.6
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 79 KYDMKKIIEFPG------FNVRPPKGTWP 101
++DM+ + + G F+ R K TWP
Sbjct: 77 RHDMEALKRYDGKYWRALFDSRVGKTTWP 105
>gnl|CDD|215137 PLN02246, PLN02246, 4-coumarate--CoA ligase.
Length = 537
Score = 28.0 bits (63), Expect = 6.9
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 5/29 (17%)
Query: 68 DEDGEI-EVDRCKYDMKKIIEFPGFNVRP 95
D+D E+ VDR +K++I++ GF V P
Sbjct: 423 DDDDELFIVDR----LKELIKYKGFQVAP 447
>gnl|CDD|213272 cd05904, 4CL, 4-Coumarate-CoA Ligase (4CL). 4-Coumarate:coenzyme A
ligase is a key enzyme in the phenylpropanoid metabolic
pathway for monolignol and flavonoid biosynthesis. It
catalyzes the synthesis of hydroxycinnamate-CoA
thioesters in a two-step reaction, involving the
formation of hydroxycinnamate-AMP anhydride and the
nucleophilic substitution of AMP by CoA. The
phenylpropanoid pathway is one of the most important
secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 504
Score = 28.0 bits (63), Expect = 7.3
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 5/29 (17%)
Query: 68 DEDGEIE-VDRCKYDMKKIIEFPGFNVRP 95
DEDG + VDR +K++I++ GF V P
Sbjct: 397 DEDGYLFIVDR----LKELIKYKGFQVAP 421
>gnl|CDD|227134 COG4797, COG4797, Predicted regulatory domain of a
methyltransferase [General function prediction only].
Length = 268
Score = 27.5 bits (61), Expect = 8.7
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 48 QYYDYKTPRSFKTVTLADPEDEDGEIEVDRCKYDMKKIIEFPGFNVRPPKG 98
QY D+ T R F+T L E+ +I + + + ++ N+RP +G
Sbjct: 33 QYMDFITNRQFRTSLLC---HEENKINRNISEDVAIEFLK--SINIRPARG 78
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
0.323 0.142 0.427
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,748,153
Number of extensions: 1446837
Number of successful extensions: 1370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1368
Number of HSP's successfully gapped: 32
Length of query: 278
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 182
Effective length of database: 6,679,618
Effective search space: 1215690476
Effective search space used: 1215690476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)