RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020234
(329 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 726 bits (1875), Expect = 0.0
Identities = 299/329 (90%), Positives = 315/329 (95%)
Query: 1 MGGCKGPITTFIVEPFVPHNQEYYLSIVSDRLGCTISFSECGGIEIEENWDKVKTIFLPT 60
MGGCKGPITTFIVEPFVPH+QE+YLSIVSDRLGC+ISFSECGGIEIEENWDKVKTIFLPT
Sbjct: 95 MGGCKGPITTFIVEPFVPHDQEFYLSIVSDRLGCSISFSECGGIEIEENWDKVKTIFLPT 154
Query: 61 EKHMTLDACAPLIATLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDM 120
E +T + CAPLIATLPLE RGKI +FI GVFAVFQDLDF+F+EMNPFTLV+GEPYPLDM
Sbjct: 155 EAPLTSEICAPLIATLPLEIRGKIEEFIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDM 214
Query: 121 RGELDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWT 180
RGELDDTAAFKNFKKW NIEFPLPFGRV+S TESFIH LDEKTSASLKFTVLNPKGRIWT
Sbjct: 215 RGELDDTAAFKNFKKWGNIEFPLPFGRVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWT 274
Query: 181 MVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRA 240
MVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATA+PDGRKRA
Sbjct: 275 MVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATANPDGRKRA 334
Query: 241 LLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEE 300
LLIGGGIANFTDVA TFNGIIRALREKESKLKAARMHIFVRRGGPNYQ GLAKMRALGEE
Sbjct: 335 LLIGGGIANFTDVAATFNGIIRALREKESKLKAARMHIFVRRGGPNYQKGLAKMRALGEE 394
Query: 301 LGIPLEVYGPEATMTGICKQAIDCIMSAS 329
+G+P+EVYGPEATMTGICKQAID I +A+
Sbjct: 395 IGVPIEVYGPEATMTGICKQAIDYITAAA 423
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 133 bits (338), Expect = 4e-36
Identities = 77/318 (24%), Positives = 120/318 (37%), Gaps = 44/318 (13%)
Query: 6 GPITTFIVEPFVPH-NQEYYLSIVSDRLGCTISF--SECGGIEIEE----NWDKVKTIFL 58
P+ +VE V +EYYLSIV DR S GG++IEE +K+ + +
Sbjct: 88 EPVNKVLVEEAVDIIKKEYYLSIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSV 147
Query: 59 PTEKHMTLDACAPLIAT---LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPF--TLVNG 113
+ A +A L E ++ D I ++ +F + D + +E+NP T G
Sbjct: 148 DPLTGLR-PYQARELAFKLGLEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGG 206
Query: 114 EPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLN 173
+ LD + LDD A F P L E + L + L+
Sbjct: 207 DVLALDAKITLDDNA-----------LFRHPDLAELRDESEEDPREAEASGYGLNYVELD 255
Query: 174 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATAD 233
G I +V G G ++ D V G + N+ + G E V + +D
Sbjct: 256 --GNIGCIVNGAGLAMATMDIVKLYG--GKPANFLDVGGGATAERV----KEAFKLILSD 307
Query: 234 PDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAK 293
P+ + + I GGI T GII AL+E + + VR G N + G
Sbjct: 308 PNVKAIFVNIFGGI---TRCDEVAEGIIAALKEVGVNVP-----LVVRLEGTNVEEGKRI 359
Query: 294 MRALGEELGIPLEVYGPE 311
+ E G+ +
Sbjct: 360 LA----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 = 75.5 bits (186), Expect = 3e-15
Identities = 79/330 (23%), Positives = 137/330 (41%), Gaps = 45/330 (13%)
Query: 7 PITTFIVEPFVPHNQEYYLSIVSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPT 60
P+ ++E ++EYYLSIV DR I S GG++IEE + +K+ +
Sbjct: 92 PVNKILIEEATDIDKEYYLSIVIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDP 151
Query: 61 EKHMTLDACAPLIA---TLPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPY 116
+ L A IA L E ++ D I ++ +F + D S +E+NP + +G
Sbjct: 152 LTGL-LPYQAREIAKKLGLEGELVKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLI 210
Query: 117 PLDMRGELDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKG 176
LD + +DD A F++ + S E L ++ L + L+ G
Sbjct: 211 ALDAKLTIDDNALFRH-PDLEEMRDY--------SQEDPREVLAKQ--WGLNYVALD--G 257
Query: 177 RIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDG 236
I MV G G ++ D + G E N+ + G + E V + ++V+ +D
Sbjct: 258 NIGCMVNGAGLAMATMDIIKLYG--GEPANFLDVGGGASAERVREALKLVL----SDKSV 311
Query: 237 RKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRA 296
+ + I GGI VA G++ AL+E + + VR G N + G +
Sbjct: 312 KVVFINIFGGITRCDLVA---KGLVEALKEVGVNVP-----VVVRLEGTNVEEGKKILA- 362
Query: 297 LGEELGIPLEVYGPEATMTGICKQAIDCIM 326
E G+ + +M ++A++
Sbjct: 363 ---ESGLNII---FATSMEEAAEKAVEAAE 386
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 57.4 bits (140), Expect = 3e-09
Identities = 42/131 (32%), Positives = 62/131 (47%), Gaps = 15/131 (11%)
Query: 13 VEPFVPHNQEYYLSIVSDRLGCTISF--SECGGIEIEE----NWDKVKTIFLPTEKHMTL 66
VE +EYYLSIV DR + F S GG++IEE +K+ + + +
Sbjct: 98 VEEGADIAKEYYLSIVLDRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQ- 156
Query: 67 DACAPLIAT---LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV---NGEPYPLDM 120
A IA LP E + +MG++ F + D S +E+NP LV +G+ LD
Sbjct: 157 PFQAREIAFKLGLPGEQVKQFAKILMGLYKAFVEKDASLVEINP--LVVTKDGDLIALDA 214
Query: 121 RGELDDTAAFK 131
+ DD A F+
Sbjct: 215 KINFDDNALFR 225
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 51.1 bits (123), Expect = 1e-07
Identities = 33/105 (31%), Positives = 50/105 (47%), Gaps = 10/105 (9%)
Query: 13 VEPFVPHNQEYYLSIVSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTL 66
VE V +EYYLSIV DR G + S GG++IEE N + + + + +T
Sbjct: 97 VEEAVDIAREYYLSIVLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLT- 155
Query: 67 DACAPLIAT---LPLEFRGKIGDFIMGVFAVFQDLDFSFIEMNPF 108
A IA L E + D I ++ +F + D + +E+NP
Sbjct: 156 PYQAREIAFKLGLEGELVKQAADIIKKLYKLFVERDATLVEINPL 200
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 42.4 bits (100), Expect = 2e-04
Identities = 76/313 (24%), Positives = 123/313 (39%), Gaps = 50/313 (15%)
Query: 7 PITTFIVEPFVPHNQEYYLSIVSDRLG--CTISFSECGGIEIEE----NWDKVKTIFLPT 60
P+ VE P +E YL V DR + S GG+EIEE + + + +
Sbjct: 92 PVQRVYVETADPIERELYLGFVLDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEP 151
Query: 61 EKHMTLDACAPLIATLPLEFR--GKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYP 117
+ + L L+ + + IMG + F+DLD + +E+NP + +
Sbjct: 152 AVGLQQFQAREIAFGLGLDIKQVSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLA 211
Query: 118 LDMRGELDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLD---EKTSASLKFTVLNP 174
LD + DD A F+ NI E S + E +A + +
Sbjct: 212 LDAKMSFDDNALFRR----PNI------------AEMRDPSQEDPREAQAAEHGLSYVGL 255
Query: 175 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADP 234
G I +V G G ++ D + G E N+ + G + E V + R+V+
Sbjct: 256 DGDIGCIVNGAGLAMATMDMIKLAG--GEPANFLDVGGGASPERVAKAFRLVLS------ 307
Query: 235 DGRKRALL--IGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLA 292
D +A+L I GI VA G+++A RE + + VR G N + G
Sbjct: 308 DRNVKAILVNIFAGINRCDWVA---EGVVQAAREVGIDVP-----LVVRLAGTNVEEG-- 357
Query: 293 KMRALGEELGIPL 305
R + E G+P+
Sbjct: 358 --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 = 0.34
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 98 LDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFK---KW 136
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 = 1.6
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 122 GELDDTAAFKNFKKWANIE-------FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNP 174
E+D ++N K+ + +P F R ++ E D + L+ T+LN
Sbjct: 78 AEVDPRLYYENRSKFIQEQKAKGINPYPHKFERTITVPEFVEKYQDLASGEHLEDTILNV 137
Query: 175 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 208
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 = 28.7 bits (65), Expect = 3.6
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 207 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 247
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 = 3.6
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 234 PDGRKRALLIGGGIANFTDVATTFNGI--IRALREKESKLKAAR-MHIFVRRGGPNYQTG 290
D R R + I GGI GI AL E + AR + +F P
Sbjct: 92 DDRRARQIWIAGGI-----------GITPFLALLEALAARGDARPVTLFYCVRDPEDAVF 140
Query: 291 LAKMRALGEELGIPLEV 307
L ++RAL G+ L V
Sbjct: 141 LDELRALAAAAGVVLHV 157
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.2 bits (66), Expect = 3.7
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 169 FTVLNPKGRIWTMVAGGGASVIYADTVG 196
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 = 4.8
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 137 ANIEFPLP-------FGRVLS 150
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 = 28.3 bits (63), Expect = 7.3
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 174 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDC---- 229
P GR+W G G+++ A GN + P EV +
Sbjct: 438 PAGRLWICTDGNGSTLGVTPEGNVYNLARNDGNNGMLTEGPIRGEVKLFLTGPEGSEFTG 497
Query: 230 ATADPDGR 237
T PDGR
Sbjct: 498 PTFSPDGR 505
>gnl|CDD|223999 COG1073, COG1073, Hydrolases of the alpha/beta superfamily [General
function prediction only].
Length = 299
Score = 27.8 bits (61), Expect = 8.8
Identities = 21/186 (11%), Positives = 39/186 (20%), Gaps = 3/186 (1%)
Query: 114 EPYPLDMRGELDDTAAFKNFKKWANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLN 173
+ + L + KK + F FG + + L EK L
Sbjct: 27 NRTGIALAAVLHLPPSGNEEKKLPAVVFLHGFGSSKEQSLGYAVLLAEKGYRVLAGDASL 86
Query: 174 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNY--AEYSGAPNEEEVLQYARVVIDCAT 231
G S YA+ +Y A + + +
Sbjct: 87 FGESGGDP-RGLADSEGYAEDFSAAVLLLLSEGVLDKDYRLLGASLGPRILAGLSLGGPS 145
Query: 232 ADPDGRKRALLIGGGIANFTDVATTFNGIIRALREKESKLKAARMHIFVRRGGPNYQTGL 291
A + + + L + ++ G
Sbjct: 146 AGALLAWGPTRLDASRIVVWGESLGGALALLLLGANPELARELIDYLITPGGFAPLPAPE 205
Query: 292 AKMRAL 297
A + L
Sbjct: 206 APLDTL 211
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 0.139 0.419
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: 17,287,887
Number of extensions: 1727477
Number of successful extensions: 1710
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1695
Number of HSP's successfully gapped: 26
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
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: 59 (26.4 bits)