RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014514
(423 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 921 bits (2382), Expect = 0.0
Identities = 383/423 (90%), Positives = 403/423 (95%)
Query: 1 MARKKIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPD 60
MARKKIREYDSKRLLKEHLKRLAG+DL I SAQVTESTDF+EL NKEPWLSS++LVVKPD
Sbjct: 1 MARKKIREYDSKRLLKEHLKRLAGIDLPIRSAQVTESTDFNELANKEPWLSSTKLVVKPD 60
Query: 61 MLFGKRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKGPITTFIVEPFVPHNQEYYLS 120
MLFGKRGKSGLVALNLDLAQVA FVK RLG EVEMGGCKGPITTFIVEPFVPH+QE+YLS
Sbjct: 61 MLFGKRGKSGLVALNLDLAQVATFVKERLGKEVEMGGCKGPITTFIVEPFVPHDQEFYLS 120
Query: 121 IVSDRLGCTISFSECGGIEIEENWDKVKTIFLPTEKHMTLDACAPLIATLPLEFRGKIGD 180
IVSDRLGC+ISFSECGGIEIEENWDKVKTIFLPTE +T + CAPLIATLPLE RGKI +
Sbjct: 121 IVSDRLGCSISFSECGGIEIEENWDKVKTIFLPTEAPLTSEICAPLIATLPLEIRGKIEE 180
Query: 181 FIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFG 240
FI GVFAVFQDLDF+F+EMNPFTLV+GEPYPLDMRGELDDTAAFKNFKKW NIEFPLPFG
Sbjct: 181 FIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGELDDTAAFKNFKKWGNIEFPLPFG 240
Query: 241 RVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN 300
RV+S TESFIH LDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN
Sbjct: 241 RVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN 300
Query: 301 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 360
YAEYSGAPNEEEVLQYARVVIDCATA+PDGRKRALLIGGGIANFTDVA TFNGIIRALRE
Sbjct: 301 YAEYSGAPNEEEVLQYARVVIDCATANPDGRKRALLIGGGIANFTDVAATFNGIIRALRE 360
Query: 361 KESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 420
KESKLKAARMHIFVRRGGPNYQ GLAKMRALGEE+G+P+EVYGPEATMTGICKQAID I
Sbjct: 361 KESKLKAARMHIFVRRGGPNYQKGLAKMRALGEEIGVPIEVYGPEATMTGICKQAIDYIT 420
Query: 421 SAS 423
+A+
Sbjct: 421 AAA 423
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 170 bits (434), Expect = 4e-49
Identities = 100/413 (24%), Positives = 157/413 (38%), Gaps = 53/413 (12%)
Query: 5 KIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPDMLFG 64
+ EY +K L ++ + + V S + +E KE L +VVK + G
Sbjct: 2 NLHEYQAKELFAKY-------GIPVPPGYVATSPEEAEEAAKE--LGGGPVVVKAQVHAG 52
Query: 65 KRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKGPITTFIVEPFVPH-NQEYYLSIVS 123
RGK+G V L + E + LG + P+ +VE V +EYYLSIV
Sbjct: 53 GRGKAGGVKLAKSPEEAKEAAEEILGKNYQTDIKGEPVNKVLVEEAVDIIKKEYYLSIVL 112
Query: 124 DRLGCTISF--SECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LPLEF 174
DR S GG++IEE +K+ + + + A +A L E
Sbjct: 113 DRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLR-PYQARELAFKLGLEGEL 171
Query: 175 RGKIGDFIMGVFAVFQDLDFSFIEMNPF--TLVNGEPYPLDMRGELDDTAAFKNFKKWAN 232
++ D I ++ +F + D + +E+NP T G+ LD + LDD A
Sbjct: 172 VKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNA---------- 221
Query: 233 IEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDL 292
F P L E + L + L+ G I +V G G ++ D V
Sbjct: 222 -LFRHPDLAELRDESEEDPREAEASGYGLNYVELD--GNIGCIVNGAGLAMATMDIVKLY 278
Query: 293 GYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFN 352
G + N+ + G E V + +DP+ + + I GGI T
Sbjct: 279 G--GKPANFLDVGGGATAERV----KEAFKLILSDPNVKAIFVNIFGGI---TRCDEVAE 329
Query: 353 GIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPE 405
GII AL+E + + VR G N + G + E G+ +
Sbjct: 330 GIIAALKEVGVNVP-----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 = 99.8 bits (249), Expect = 4e-23
Identities = 98/429 (22%), Positives = 175/429 (40%), Gaps = 57/429 (13%)
Query: 5 KIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPDMLFG 64
+ EY +K++ ++ + + V S + +E + L + +VVK + G
Sbjct: 2 NLHEYQAKQIFAKY-------GIPVPRGYVATSVEEAEEIAAK--LGAGPVVVKAQVHAG 52
Query: 65 KRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKG---PITTFIVEPFVPHNQEYYLSI 121
RGK+G V + + + LG E+ P+ ++E ++EYYLSI
Sbjct: 53 GRGKAGGVKVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLSI 112
Query: 122 VSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIA---TLPL 172
V DR I S GG++IEE + +K+ + + L A IA L
Sbjct: 113 VIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGL-LPYQAREIAKKLGLEG 171
Query: 173 EFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFKNFKKWA 231
E ++ D I ++ +F + D S +E+NP + +G LD + +DD A F++
Sbjct: 172 ELVKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRH-PDLE 230
Query: 232 NIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGD 291
+ S E L ++ L + L+ G I MV G G ++ D +
Sbjct: 231 EMRDY--------SQEDPREVLAKQ--WGLNYVALD--GNIGCMVNGAGLAMATMDIIKL 278
Query: 292 LGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTF 351
G E N+ + G + E V + ++V+ +D + + I GGI VA
Sbjct: 279 YG--GEPANFLDVGGGASAERVREALKLVL----SDKSVKVVFINIFGGITRCDLVA--- 329
Query: 352 NGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGI 411
G++ AL+E + + VR G N + G + E G+ + +M
Sbjct: 330 KGLVEALKEVGVNVP-----VVVRLEGTNVEEGKKILA----ESGLNII---FATSMEEA 377
Query: 412 CKQAIDCIM 420
++A++
Sbjct: 378 AEKAVEAAE 386
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 77.3 bits (191), Expect = 2e-16
Identities = 62/210 (29%), Positives = 97/210 (46%), Gaps = 22/210 (10%)
Query: 5 KIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPDMLFG 64
+ EY +K LL ++ G+ + +V S + +E K+ L VVK +L G
Sbjct: 1 NLHEYQAKELLAKY-----GVPVPR--GEVAFSPEEAEEAAKK--LGGKVWVVKAQVLAG 51
Query: 65 KRGKSGLVALNLDLAQVAEFVKGRLGTEV--EMGGCKG-PITTFIVEPFVPHNQEYYLSI 121
RGK+G V L + E K LG + + G +G P+ +VE V +EYYLSI
Sbjct: 52 GRGKAGGVKLAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSI 111
Query: 122 VSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LPL 172
V DR G + S GG++IEE N + + + + +T A IA L
Sbjct: 112 VLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLT-PYQAREIAFKLGLEG 170
Query: 173 EFRGKIGDFIMGVFAVFQDLDFSFIEMNPF 202
E + D I ++ +F + D + +E+NP
Sbjct: 171 ELVKQAADIIKKLYKLFVERDATLVEINPL 200
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 76.3 bits (189), Expect = 3e-15
Identities = 68/236 (28%), Positives = 104/236 (44%), Gaps = 27/236 (11%)
Query: 5 KIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPDMLFG 64
+ EY +K L ++ + + V + + + +E L VVK + G
Sbjct: 2 NLHEYQAKELFAKY-------GVPVPRGIVATTPEEAVEAAEE--LGGGVWVVKAQVHAG 52
Query: 65 KRGKSGLVALNLDLAQVAEFVKGRLGTEVE--MGGCKG-PITTFIVEPFVPHNQEYYLSI 121
RGK+G V L + EF K LG + G KG P+ +VE +EYYLSI
Sbjct: 53 GRGKAGGVKLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKEYYLSI 112
Query: 122 VSDRLGCTISF--SECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LPL 172
V DR + F S GG++IEE +K+ + + + A IA LP
Sbjct: 113 VLDRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQ-PFQAREIAFKLGLPG 171
Query: 173 EFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV---NGEPYPLDMRGELDDTAAFK 225
E + +MG++ F + D S +E+NP LV +G+ LD + DD A F+
Sbjct: 172 EQVKQFAKILMGLYKAFVEKDASLVEINP--LVVTKDGDLIALDAKINFDDNALFR 225
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 56.6 bits (137), Expect = 1e-08
Identities = 99/411 (24%), Positives = 162/411 (39%), Gaps = 62/411 (15%)
Query: 6 IREYDSKRLLKEHLKRLAGLDLQICSAQVTESTDFSELTNKEPWLSSSRLVVKPDMLFGK 65
I EY +K LL A + + + S + + +E L VVK + G
Sbjct: 3 IHEYQAKELL-------ASFGVAVPRGALAYSPEQAVYRARE--LGGWHWVVKAQIHSGA 53
Query: 66 RGKSGLVALNLDLAQVAEFVKGRLGTEV---EMGGCKGPITTFIVEPFVPHNQEYYLSIV 122
RGK+G + L +V + + LG ++ + G P+ VE P +E YL V
Sbjct: 54 RGKAGGIKLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLGFV 113
Query: 123 SDRLG--CTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIATLPLEFR- 175
DR + S GG+EIEE + + + + + + L L+ +
Sbjct: 114 LDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDIKQ 173
Query: 176 -GKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFKNFKKWANI 233
+ IMG + F+DLD + +E+NP + + LD + DD A F+ NI
Sbjct: 174 VSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFRR----PNI 229
Query: 234 EFPLPFGRVLSSTESFIHSLD---EKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVG 290
E S + E +A + + G I +V G G ++ D +
Sbjct: 230 ------------AEMRDPSQEDPREAQAAEHGLSYVGLDGDIGCIVNGAGLAMATMDMIK 277
Query: 291 DLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALL--IGGGIANFTDVA 348
G E N+ + G + E V + R+V+ D +A+L I GI VA
Sbjct: 278 LAG--GEPANFLDVGGGASPERVAKAFRLVLS------DRNVKAILVNIFAGINRCDWVA 329
Query: 349 TTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPL 399
G+++A RE + + VR G N + G R + E G+P+
Sbjct: 330 ---EGVVQAAREVGIDVP-----LVVRLAGTNVEEG----RKILAESGLPI 368
>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 = 0.54
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 192 LDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFK---KW 230
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 = 2.3
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 216 GELDDTAAFKNFKKWANIE-------FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNP 268
E+D ++N K+ + +P F R ++ E D + L+ T+LN
Sbjct: 78 AEVDPRLYYENRSKFIQEQKAKGINPYPHKFERTITVPEFVEKYQDLASGEHLEDTILNV 137
Query: 269 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 302
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 = 29.1 bits (66), Expect = 3.8
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 301 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 341
Y EYSGA EV++ + V+ L++GGGI
Sbjct: 153 YLEYSGAYGPPEVVRAVKKVLG---------DTPLIVGGGI 184
>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 = 28.8 bits (65), Expect = 4.0
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 328 PDGRKRALLIGGGIANFTDVATTFNGI--IRALREKESKLKAAR-MHIFVRRGGPNYQTG 384
D R R + I GGI GI AL E + AR + +F P
Sbjct: 92 DDRRARQIWIAGGI-----------GITPFLALLEALAARGDARPVTLFYCVRDPEDAVF 140
Query: 385 LAKMRALGEELGIPLEV 401
L ++RAL G+ L V
Sbjct: 141 LDELRALAAAAGVVLHV 157
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 29.2 bits (65), Expect = 5.8
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 1 MARKKIREYDSKRLLKEHLKRLAGLDLQICSAQVTESTD-FSELTNKEPW----LSSSRL 55
M KKI Y+ K L E G D +C+ + E + + N E W L SS L
Sbjct: 567 MILKKIYVYNEKELYDEDKTAKQGKDKFLCTHYLKEREERICFIQNSEHWDNLVLGSSDL 626
>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 = 28.7 bits (64), Expect = 7.3
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 268 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDC---- 323
P GR+W G G+++ A GN + P EV +
Sbjct: 438 PAGRLWICTDGNGSTLGVTPEGNVYNLARNDGNNGMLTEGPIRGEVKLFLTGPEGSEFTG 497
Query: 324 ATADPDGR 331
T PDGR
Sbjct: 498 PTFSPDGR 505
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.4 bits (64), Expect = 7.8
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 263 FTVLNPKGRIWTMVAGGGASVIYADTVG 290
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 = 8.1
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 231 ANIEFPLP-------FGRVLS 244
ANI+FPLP F RVL
Sbjct: 58 ANIDFPLPATFIWDMFTRVLP 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
0.320 0.138 0.407
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: 22,043,436
Number of extensions: 2202094
Number of successful extensions: 2108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2086
Number of HSP's successfully gapped: 25
Length of query: 423
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 323
Effective length of database: 6,502,202
Effective search space: 2100211246
Effective search space used: 2100211246
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: 60 (26.8 bits)