RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 024560
(266 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 579 bits (1495), Expect = 0.0
Identities = 241/266 (90%), Positives = 254/266 (95%)
Query: 1 MTLDACAPLIATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGE 60
+T + CAPLIATLPLE RGKI +FI GVFAVFQDLDF+F+EMNPFTLV+GEPYPLDMRGE
Sbjct: 158 LTSEICAPLIATLPLEIRGKIEEFIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGE 217
Query: 61 LDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVA 120
LDDTAAFKNFKKW NIEFPLPFGRV+S TESFIH LDEKTSASLKFTVLNPKGRIWTMVA
Sbjct: 218 LDDTAAFKNFKKWGNIEFPLPFGRVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVA 277
Query: 121 GGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLI 180
GGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATA+PDGRKRALLI
Sbjct: 278 GGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATANPDGRKRALLI 337
Query: 181 GGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGI 240
GGGIANFTDVA TFNGIIRALREKESKLKAARMHIFVRRGGPNYQ GLAKMRALGEE+G+
Sbjct: 338 GGGIANFTDVAATFNGIIRALREKESKLKAARMHIFVRRGGPNYQKGLAKMRALGEEIGV 397
Query: 241 PLEVYGPEATMTGICKQAIDCIMSAS 266
P+EVYGPEATMTGICKQAID I +A+
Sbjct: 398 PIEVYGPEATMTGICKQAIDYITAAA 423
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 93.8 bits (234), Expect = 4e-22
Identities = 55/238 (23%), Positives = 87/238 (36%), Gaps = 33/238 (13%)
Query: 13 LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPF--TLVNGEPYPLDMRGELDDTAAFKNF 70
L E ++ D I ++ +F + D + +E+NP T G+ LD + LDD A
Sbjct: 167 LEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNA----- 221
Query: 71 KKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYAD 130
F P L E + L + L+ G I +V G G ++ D
Sbjct: 222 ------LFRHPDLAELRDESEEDPREAEASGYGLNYVELD--GNIGCIVNGAGLAMATMD 273
Query: 131 TVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDV 190
V G + N+ + G E V + +DP+ + + I GGI T
Sbjct: 274 IVKLYG--GKPANFLDVGGGATAERV----KEAFKLILSDPNVKAIFVNIFGGI---TRC 324
Query: 191 ATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPE 248
GII AL+E + + VR G N + G + E G+ +
Sbjct: 325 DEVAEGIIAALKEVGVNVP-----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 = 50.1 bits (120), Expect = 4e-07
Identities = 56/252 (22%), Positives = 102/252 (40%), Gaps = 35/252 (13%)
Query: 13 LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFKNFK 71
L E ++ D I ++ +F + D S +E+NP + +G LD + +DD A F++
Sbjct: 169 LEGELVKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRH-P 227
Query: 72 KWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADT 131
+ S E L ++ L + L+ G I MV G G ++ D
Sbjct: 228 DLEEMRDY--------SQEDPREVLAKQ--WGLNYVALD--GNIGCMVNGAGLAMATMDI 275
Query: 132 VGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVA 191
+ G E N+ + G + E V + ++V+ +D + + I GGI VA
Sbjct: 276 IKLYG--GEPANFLDVGGGASAERVREALKLVL----SDKSVKVVFINIFGGITRCDLVA 329
Query: 192 TTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATM 251
G++ AL+E + + VR G N + G + E G+ + +M
Sbjct: 330 ---KGLVEALKEVGVNVP-----VVVRLEGTNVEEGKKILA----ESGLNII---FATSM 374
Query: 252 TGICKQAIDCIM 263
++A++
Sbjct: 375 EEAAEKAVEAAE 386
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 36.6 bits (86), Expect = 0.010
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 13 LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV---NGEPYPLDMRGELDDTAAFK 68
LP E + +MG++ F + D S +E+NP LV +G+ LD + DD A F+
Sbjct: 169 LPGEQVKQFAKILMGLYKAFVEKDASLVEINP--LVVTKDGDLIALDAKINFDDNALFR 225
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 33.5 bits (77), Expect = 0.11
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 25 IMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFK 68
IMG + F+DLD + +E+NP + + LD + DD A F+
Sbjct: 181 IMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFR 225
>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 = 0.27
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 35 LDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFK---KW 73
L+ +F+ + PF+L + Y +++ L+D +NF KW
Sbjct: 204 LNLTFLMLKPFSL-GYQKY-VNLVDILEDERKVENFLRMEKW 243
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 30.4 bits (68), Expect = 0.99
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 59 GELDDTAAFKNFKKWANIE-------FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNP 111
E+D ++N K+ + +P F R ++ E D + L+ T+LN
Sbjct: 78 AEVDPRLYYENRSKFIQEQKAKGINPYPHKFERTITVPEFVEKYQDLASGEHLEDTILNV 137
Query: 112 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 145
GRI V+ G + + D VGD L N+A
Sbjct: 138 TGRI-MRVSASGQKLRFFDLVGDGAKIQVLANFA 170
>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 = 3.2
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 144 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 184
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 = 3.4
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 106 FTVLNPKGRIWTMVAGGGASVIYADTVG 133
F L+P R + G G V+ DTVG
Sbjct: 224 FATLDPTTRR--IELGDGRKVLLTDTVG 249
>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 = 3.5
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 171 PDGRKRALLIGGGIANFTDVATTFNGI--IRALREKESKLKAAR-MHIFVRRGGPNYQTG 227
D R R + I GGI GI AL E + AR + +F P
Sbjct: 92 DDRRARQIWIAGGI-----------GITPFLALLEALAARGDARPVTLFYCVRDPEDAVF 140
Query: 228 LAKMRALGEELGIPLEV 244
L ++RAL G+ L V
Sbjct: 141 LDELRALAAAAGVVLHV 157
>gnl|CDD|236835 PRK11069, recC, exonuclease V subunit gamma; Provisional.
Length = 1122
Score = 28.7 bits (65), Expect = 4.1
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 74 ANIEFPLP-------FGRVLS 87
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 = 6.3
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 111 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDC---- 166
P GR+W G G+++ A GN + P EV +
Sbjct: 438 PAGRLWICTDGNGSTLGVTPEGNVYNLARNDGNNGMLTEGPIRGEVKLFLTGPEGSEFTG 497
Query: 167 ATADPDGR 174
T PDGR
Sbjct: 498 PTFSPDGR 505
>gnl|CDD|183946 PRK13282, PRK13282, flagellar assembly protein FliW; Provisional.
Length = 128
Score = 26.5 bits (59), Expect = 8.1
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 12/76 (15%)
Query: 1 MTLDACAPL-----IATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGE---P 52
M D +P+ I + LE KI + + + + FSF +NPF L E P
Sbjct: 1 MIFDVKSPILGFETIKKMELE---KIDEVFVRLKSA-DGNSFSFTLINPFALREYEFEIP 56
Query: 53 YPLDMRGELDDTAAFK 68
EL++ +
Sbjct: 57 TYYKELLELEEASNLL 72
>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 = 8.5
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 145 AEYSGAPNEEEVLQYARVVID 165
A Y N+E VL YA+ +ID
Sbjct: 21 ARYKADINQETVLNYAQEIID 41
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 0.411
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,033,225
Number of extensions: 1390844
Number of successful extensions: 1488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1483
Number of HSP's successfully gapped: 32
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
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 (26.0 bits)