RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 026236
(241 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 535 bits (1381), Expect = 0.0
Identities = 223/241 (92%), Positives = 233/241 (96%)
Query: 1 MGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGRV 60
GVFAVFQDLDF+F+EMNPFTLV+GEPYPLDMRGELDDTAAFKNFKKW NIEFPLPFGRV
Sbjct: 183 KGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGELDDTAAFKNFKKWGNIEFPLPFGRV 242
Query: 61 LSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 120
+S TESFIH LDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYA
Sbjct: 243 MSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 302
Query: 121 EYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKE 180
EYSGAPNEEEVLQYARVVIDCATA+PDGRKRALLIGGGIANFTDVA TFNGIIRALREKE
Sbjct: 303 EYSGAPNEEEVLQYARVVIDCATANPDGRKRALLIGGGIANFTDVAATFNGIIRALREKE 362
Query: 181 SKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIMSA 240
SKLKAARMHIFVRRGGPNYQ GLAKMRALGEE+G+P+EVYGPEATMTGICKQAID I +A
Sbjct: 363 SKLKAARMHIFVRRGGPNYQKGLAKMRALGEEIGVPIEVYGPEATMTGICKQAIDYITAA 422
Query: 241 S 241
+
Sbjct: 423 A 423
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 85.7 bits (213), Expect = 2e-19
Identities = 51/225 (22%), Positives = 81/225 (36%), Gaps = 33/225 (14%)
Query: 1 MGVFAVFQDLDFSFIEMNPF--TLVNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFG 58
++ +F + D + +E+NP T G+ LD + LDD A F P
Sbjct: 180 KKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNA-----------LFRHPDL 228
Query: 59 RVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN 118
L E + L + L+ G I +V G G ++ D V G + N
Sbjct: 229 AELRDESEEDPREAEASGYGLNYVELD--GNIGCIVNGAGLAMATMDIVKLYG--GKPAN 284
Query: 119 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 178
+ + G E V + +DP+ + + I GGI T GII AL+E
Sbjct: 285 FLDVGGGATAERV----KEAFKLILSDPNVKAIFVNIFGGI---TRCDEVAEGIIAALKE 337
Query: 179 KESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPE 223
+ + VR G N + G + E G+ +
Sbjct: 338 VGVNVP-----LVVRLEGTNVEEGKRILA----ESGLNIIAADDL 373
>gnl|CDD|233234 TIGR01016, sucCoAbeta, succinyl-CoA synthetase, beta subunit. This
model is designated subfamily because it does not
discriminate the ADP-forming enzyme ((EC 6.2.1.5) from
the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half
is described by the CoA-ligases model (pfam00549). The
C-terminal half is described by the ATP-grasp model
(pfam02222). This family contains a split seen both in a
maximum parsimony tree (which ignores gaps) and in the
gap pattern near position 85 of the seed alignment.
Eukaryotic and most bacterial sequences are longer and
contain a region similar to TXQTXXXG. Sequences from
Deinococcus radiodurans, Mycobacterium tuberculosis,
Streptomyces coelicolor, and the Archaea are 6 amino
acids shorter in that region and contain a motif
resembling [KR]G [Energy metabolism, TCA cycle].
Length = 386
Score = 43.9 bits (104), Expect = 3e-05
Identities = 52/239 (21%), Positives = 96/239 (40%), Gaps = 35/239 (14%)
Query: 1 MGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGR 59
++ +F + D S +E+NP + +G LD + +DD A F++ +
Sbjct: 182 KKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRH-PDLEEMRDY----- 235
Query: 60 VLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGNY 119
S E L ++ L + L+ G I MV G G ++ D + G E N+
Sbjct: 236 ---SQEDPREVLAKQ--WGLNYVALD--GNIGCMVNGAGLAMATMDIIKLYG--GEPANF 286
Query: 120 AEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALREK 179
+ G + E V + ++V+ +D + + I GGI VA G++ AL+E
Sbjct: 287 LDVGGGASAERVREALKLVL----SDKSVKVVFINIFGGITRCDLVA---KGLVEALKEV 339
Query: 180 ESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 238
+ + VR G N + G + E G+ + +M ++A++
Sbjct: 340 GVNVP-----VVVRLEGTNVEEGKKILA----ESGLNII---FATSMEEAAEKAVEAAE 386
>gnl|CDD|130895 TIGR01836, PHA_synth_III_C, poly(R)-hydroxyalkanoic acid synthase,
class III, PhaC subunit. This model represents the PhaC
subunit of a heterodimeric form of polyhydroxyalkanoic
acid (PHA) synthase. Excepting the PhaC of Bacillus
megaterium (which needs PhaR), all members require PhaE
(TIGR01834) for activity and are designated class III.
This enzyme builds ester polymers for carbon and energy
storage that accumulate in inclusions, and both this
enzyme and the depolymerase associate with the
inclusions. Class III enzymes polymerize
short-chain-length hydroxyalkanoates [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 350
Score = 32.0 bits (73), Expect = 0.23
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 10 LDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFK---KW 48
L+ +F+ + PF+L + Y +++ L+D +NF KW
Sbjct: 204 LNLTFLMLKPFSL-GYQKY-VNLVDILEDERKVENFLRMEKW 243
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 31.2 bits (71), Expect = 0.41
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 1 MGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFK 43
MG + F+DLD + +E+NP + + LD + DD A F+
Sbjct: 182 MGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFR 225
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 30.4 bits (68), Expect = 0.84
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 34 GELDDTAAFKNFKKWANIE-------FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNP 86
E+D ++N K+ + +P F R ++ E D + L+ T+LN
Sbjct: 78 AEVDPRLYYENRSKFIQEQKAKGINPYPHKFERTITVPEFVEKYQDLASGEHLEDTILNV 137
Query: 87 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 120
GRI V+ G + + D VGD L N+A
Sbjct: 138 TGRI-MRVSASGQKLRFFDLVGDGAKIQVLANFA 170
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 30.1 bits (69), Expect = 1.1
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 1 MGVFAVFQDLDFSFIEMNPFTLV---NGEPYPLDMRGELDDTAAFK 43
MG++ F + D S +E+NP LV +G+ LD + DD A F+
Sbjct: 182 MGLYKAFVEKDASLVEINP--LVVTKDGDLIALDAKINFDDNALFR 225
>gnl|CDD|99795 cd06198, FNR_like_3, NAD(P) binding domain of ferredoxin
reductase-like proteins catalyze electron transfer
between an NAD(P)-binding sub-domain of the alpha/beta
class and a discrete (usually N-terminal) domain, which
varies in orientation with respect to the NAD(P) binding
domain. The N-terminal domain may contain a flavin
prosthetic group (as in flavoenzymes) or use flavin as a
substrate. Ferredoxin is reduced in the final stage of
photosystem I. The flavoprotein Ferredoxin-NADP+
reductase transfers electrons from reduced ferredoxin to
FAD (forming FADH2 via a semiquinone intermediate) which
then transfers a hydride ion to convert NADP+ to NADPH.
Length = 216
Score = 28.4 bits (64), Expect = 2.6
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 146 PDGRKRALLIGGGIANFTDVATTFNGI--IRALREKESKLKAAR-MHIFVRRGGPNYQTG 202
D R R + I GGI GI AL E + AR + +F P
Sbjct: 92 DDRRARQIWIAGGI-----------GITPFLALLEALAARGDARPVTLFYCVRDPEDAVF 140
Query: 203 LAKMRALGEELGIPLEV 219
L ++RAL G+ L V
Sbjct: 141 LDELRALAAAAGVVLHV 157
>gnl|CDD|239206 cd02812, PcrB_like, PcrB_like proteins. One member of this family,
a protein from Archaeoglobus fulgidus, has been
characterized as a (S)-3-O-geranylgeranylglyceryl
phosphate synthase (AfGGGPS). AfGGGPS catalyzes the
formation of an ether linkage between
sn-glycerol-1-phosphate (G1P) and geranylgeranyl
diphosphate (GGPP), the committed step in archaeal lipid
biosynthesis. Therefore, it has been proposed that
PcrB-like proteins are either prenyltransferases or are
involved in lipoteichoic acid biosynthesis although the
exact function is still unknown.
Length = 219
Score = 28.4 bits (64), Expect = 2.7
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 119 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 159
Y EYSGA EV++ + V+ L++GGGI
Sbjct: 153 YLEYSGAYGPPEVVRAVKKVLG---------DTPLIVGGGI 184
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.8 bits (65), Expect = 2.9
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 81 FTVLNPKGRIWTMVAGGGASVIYADTVG 108
F L+P R + G G V+ DTVG
Sbjct: 224 FATLDPTTRR--IELGDGRKVLLTDTVG 249
>gnl|CDD|236835 PRK11069, recC, exonuclease V subunit gamma; Provisional.
Length = 1122
Score = 28.7 bits (65), Expect = 3.4
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 49 ANIEFPLP-------FGRVLS 62
ANI+FPLP F RVL
Sbjct: 58 ANIDFPLPATFIWDMFTRVLP 78
>gnl|CDD|218748 pfam05787, DUF839, Bacterial protein of unknown function (DUF839).
This family consists of several bacterial proteins of
unknown function that contain a predicted beta-propeller
repeats.
Length = 515
Score = 27.9 bits (62), Expect = 5.9
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 86 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDC---- 141
P GR+W G G+++ A GN + P EV +
Sbjct: 438 PAGRLWICTDGNGSTLGVTPEGNVYNLARNDGNNGMLTEGPIRGEVKLFLTGPEGSEFTG 497
Query: 142 ATADPDGR 149
T PDGR
Sbjct: 498 PTFSPDGR 505
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 27.2 bits (61), Expect = 7.4
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 120 AEYSGAPNEEEVLQYARVVID 140
A Y N+E VL YA+ +ID
Sbjct: 21 ARYKADINQETVLNYAQEIID 41
>gnl|CDD|131079 TIGR02024, FtcD, glutamate formiminotransferase. This model
represents the tetrahydrofolate (THF) dependent
glutamate formiminotransferase involved in the histidine
utilization pathway. This enzyme interconverts
L-glutamate and N-formimino-L-glutamate. The enzyme is
bifunctional as it also catalyzes the cyclodeaminase
reaction on N-formimino-THF, converting it to
5,10-methenyl-THF and releasing ammonia - part of the
process of regenerating THF. This model covers enzymes
from metazoa as well as gram-positive bacteria and
archaea. In humans, deficiency of this enzyme results in
a disease phenotype. The crystal structure of the enzyme
has been studied in the context of the catalytic
mechanism [Energy metabolism, Amino acids and amines].
Length = 298
Score = 27.0 bits (60), Expect = 9.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 207 RALGEELGIPLEVYGPEATM 226
+ LGEELG+P+ +Y AT
Sbjct: 113 KRLGEELGVPVYLYEEAATR 132
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 26.7 bits (60), Expect = 9.5
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 81 FTVLNPKGRIWTMVAGGGASVIYADTVG 108
F L+P R + GG V+ DTVG
Sbjct: 73 FATLDPTTRRIKL--PGGREVLLTDTVG 98
>gnl|CDD|99778 cd00322, FNR_like, Ferredoxin reductase (FNR), an FAD and NAD(P)
binding protein, was intially identified as a
chloroplast reductase activity, catalyzing the electron
transfer from reduced iron-sulfur protein ferredoxin to
NADP+ as the final step in the electron transport
mechanism of photosystem I. FNR transfers electrons from
reduced ferredoxin to FAD (forming FADH2 via a
semiquinone intermediate) and then transfers a hydride
ion to convert NADP+ to NADPH. FNR has since been shown
to utilize a variety of electron acceptors and donors
and has a variety of physiological functions including
nitrogen assimilation, dinitrogen fixation, steroid
hydroxylation, fatty acid metabolism, oxygenase
activity, and methane assimilation in many organisms.
FNR has an NAD(P)-binding sub-domain of the alpha/beta
class and a discrete (usually N-terminal) flavin
sub-domain which vary in orientation with respect to the
NAD(P) binding domain. The N-terminal moeity may contain
a flavin prosthetic group (as in flavoenzymes) or use
flavin as a substrate. Because flavins such as FAD can
exist in oxidized, semiquinone (one- electron reduced),
or fully reduced hydroquinone forms, FNR can interact
with one and 2 electron carriers. FNR has a strong
preference for NADP(H) vs NAD(H).
Length = 223
Score = 26.6 bits (59), Expect = 9.8
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 145 DPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIF 191
+ +LI GGI T F ++R L + + + +
Sbjct: 93 PLEESGPVVLIAGGIG-----ITPFRSMLRHLAADKPGGE---ITLL 131
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
0.320 0.137 0.405
Gapped
Lambda K H
0.267 0.0613 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,681,317
Number of extensions: 1240118
Number of successful extensions: 1392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1387
Number of HSP's successfully gapped: 32
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
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 (21.8 bits)
S2: 58 (26.4 bits)