RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017966
(363 letters)
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 793 bits (2050), Expect = 0.0
Identities = 330/363 (90%), Positives = 346/363 (95%)
Query: 1 MLFGKRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKGPITTFIVEPFVPHNQEYYLS 60
MLFGKRGKSGLVALNLDLAQVA FVK RLG EVEMGGCKGPITTFIVEPFVPH+QE+YLS
Sbjct: 61 MLFGKRGKSGLVALNLDLAQVATFVKERLGKEVEMGGCKGPITTFIVEPFVPHDQEFYLS 120
Query: 61 IVSDRLGCTISFSECGGIEIEENWDKVKTIFLPTEKHMTLDACAPLIATLPLEFRGKIGD 120
IVSDRLGC+ISFSECGGIEIEENWDKVKTIFLPTE +T + CAPLIATLPLE RGKI +
Sbjct: 121 IVSDRLGCSISFSECGGIEIEENWDKVKTIFLPTEAPLTSEICAPLIATLPLEIRGKIEE 180
Query: 121 FIMGVFAVFQDLDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFKKWANIEFPLPFG 180
FI GVFAVFQDLDF+F+EMNPFTLV+GEPYPLDMRGELDDTAAFKNFKKW NIEFPLPFG
Sbjct: 181 FIKGVFAVFQDLDFTFLEMNPFTLVDGEPYPLDMRGELDDTAAFKNFKKWGNIEFPLPFG 240
Query: 181 RVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN 240
RV+S TESFIH LDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN
Sbjct: 241 RVMSPTESFIHGLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGDLGYASELGN 300
Query: 241 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTFNGIIRALRE 300
YAEYSGAPNEEEVLQYARVVIDCATA+PDGRKRALLIGGGIANFTDVA TFNGIIRALRE
Sbjct: 301 YAEYSGAPNEEEVLQYARVVIDCATANPDGRKRALLIGGGIANFTDVAATFNGIIRALRE 360
Query: 301 KESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTGICKQAIDCIM 360
KESKLKAARMHIFVRRGGPNYQ GLAKMRALGEE+G+P+EVYGPEATMTGICKQAID I
Sbjct: 361 KESKLKAARMHIFVRRGGPNYQKGLAKMRALGEEIGVPIEVYGPEATMTGICKQAIDYIT 420
Query: 361 SAS 363
+A+
Sbjct: 421 AAA 423
>gnl|CDD|223123 COG0045, SucC, Succinyl-CoA synthetase, beta subunit [Energy
production and conversion].
Length = 387
Score = 153 bits (389), Expect = 4e-43
Identities = 87/354 (24%), Positives = 134/354 (37%), Gaps = 44/354 (12%)
Query: 4 GKRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKGPITTFIVEPFVPH-NQEYYLSIV 62
G RGK+G V L + E + LG + P+ +VE V +EYYLSIV
Sbjct: 52 GGRGKAGGVKLAKSPEEAKEAAEEILGKNYQTDIKGEPVNKVLVEEAVDIIKKEYYLSIV 111
Query: 63 SDRLGCTISF--SECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LPLE 113
DR S GG++IEE +K+ + + + A +A L E
Sbjct: 112 LDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSVDPLTGLR-PYQARELAFKLGLEGE 170
Query: 114 FRGKIGDFIMGVFAVFQDLDFSFIEMNPF--TLVNGEPYPLDMRGELDDTAAFKNFKKWA 171
++ D I ++ +F + D + +E+NP T G+ LD + LDD A
Sbjct: 171 LVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNA--------- 221
Query: 172 NIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVGD 231
F P L E + L + L+ G I +V G G ++ D V
Sbjct: 222 --LFRHPDLAELRDESEEDPREAEASGYGLNYVELD--GNIGCIVNGAGLAMATMDIVKL 277
Query: 232 LGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATTF 291
G + N+ + G E V + +DP+ + + I GGI T
Sbjct: 278 YG--GKPANFLDVGGGATAERV----KEAFKLILSDPNVKAIFVNIFGGI---TRCDEVA 328
Query: 292 NGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPE 345
GII AL+E + + VR G N + G + E G+ +
Sbjct: 329 EGIIAALKEVGVNVP-----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 = 85.9 bits (213), Expect = 1e-18
Identities = 88/370 (23%), Positives = 151/370 (40%), Gaps = 48/370 (12%)
Query: 4 GKRGKSGLVALNLDLAQVAEFVKGRLGTEVEMGGCKG---PITTFIVEPFVPHNQEYYLS 60
G RGK+G V + + + LG E+ P+ ++E ++EYYLS
Sbjct: 52 GGRGKAGGVKVAKSKEEARAAAEKLLGKELVTNQTDPLGQPVNKILIEEATDIDKEYYLS 111
Query: 61 IVSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIA---TLP 111
IV DR I S GG++IEE + +K+ + + L A IA L
Sbjct: 112 IVIDRSARCPVIMASTEGGVDIEEVAEKSPEKIIKYAIDPLTGL-LPYQAREIAKKLGLE 170
Query: 112 LEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFKNFKKW 170
E ++ D I ++ +F + D S +E+NP + +G LD + +DD A F++
Sbjct: 171 GELVKQVADIIKKLYQIFLEYDASLVEINPLVITKDGNLIALDAKLTIDDNALFRH-PDL 229
Query: 171 ANIEFPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNPKGRIWTMVAGGGASVIYADTVG 230
+ S E L ++ L + L+ G I MV G G ++ D +
Sbjct: 230 EEMRDY--------SQEDPREVLAKQ--WGLNYVALD--GNIGCMVNGAGLAMATMDIIK 277
Query: 231 DLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGIANFTDVATT 290
G E N+ + G + E V + ++V+ +D + + I GGI VA
Sbjct: 278 LYG--GEPANFLDVGGGASAERVREALKLVL----SDKSVKVVFINIFGGITRCDLVA-- 329
Query: 291 FNGIIRALREKESKLKAARMHIFVRRGGPNYQTGLAKMRALGEELGIPLEVYGPEATMTG 350
G++ AL+E + + VR G N + G + E G+ + +M
Sbjct: 330 -KGLVEALKEVGVNVP-----VVVRLEGTNVEEGKKILA----ESGLNII---FATSMEE 376
Query: 351 ICKQAIDCIM 360
++A++
Sbjct: 377 AAEKAVEAAE 386
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 67.8 bits (167), Expect = 2e-12
Identities = 58/177 (32%), Positives = 83/177 (46%), Gaps = 18/177 (10%)
Query: 4 GKRGKSGLVALNLDLAQVAEFVKGRLGTEVE--MGGCKG-PITTFIVEPFVPHNQEYYLS 60
G RGK+G V L + EF K LG + G KG P+ +VE +EYYLS
Sbjct: 52 GGRGKAGGVKLAKSPEEAREFAKQILGMTLVTHQTGPKGQPVNKVLVEEGADIAKEYYLS 111
Query: 61 IVSDRLGCTISF--SECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LP 111
IV DR + F S GG++IEE +K+ + + + A IA LP
Sbjct: 112 IVLDRATRRVVFMASTEGGMDIEEVAEETPEKIHKVAIDPLTGLQ-PFQAREIAFKLGLP 170
Query: 112 LEFRGKIGDFIMGVFAVFQDLDFSFIEMNPFTLV---NGEPYPLDMRGELDDTAAFK 165
E + +MG++ F + D S +E+NP LV +G+ LD + DD A F+
Sbjct: 171 GEQVKQFAKILMGLYKAFVEKDASLVEINP--LVVTKDGDLIALDAKINFDDNALFR 225
>gnl|CDD|219843 pfam08442, ATP-grasp_2, ATP-grasp domain.
Length = 202
Score = 61.5 bits (150), Expect = 4e-11
Identities = 47/151 (31%), Positives = 71/151 (47%), Gaps = 13/151 (8%)
Query: 4 GKRGKSGLVALNLDLAQVAEFVKGRLGTEV--EMGGCKG-PITTFIVEPFVPHNQEYYLS 60
G RGK+G V L + E K LG + + G +G P+ +VE V +EYYLS
Sbjct: 51 GGRGKAGGVKLAKSPEEAKEAAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLS 110
Query: 61 IVSDRL--GCTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIAT---LP 111
IV DR G + S GG++IEE N + + + + +T A IA L
Sbjct: 111 IVLDRASRGPVLIASTEGGVDIEEVAAKNPEAIHKVPIDPATGLT-PYQAREIAFKLGLE 169
Query: 112 LEFRGKIGDFIMGVFAVFQDLDFSFIEMNPF 142
E + D I ++ +F + D + +E+NP
Sbjct: 170 GELVKQAADIIKKLYKLFVERDATLVEINPL 200
>gnl|CDD|237594 PRK14046, PRK14046, malate--CoA ligase subunit beta; Provisional.
Length = 392
Score = 50.5 bits (121), Expect = 6e-07
Identities = 45/174 (25%), Positives = 75/174 (43%), Gaps = 12/174 (6%)
Query: 4 GKRGKSGLVALNLDLAQVAEFVKGRLGTEV---EMGGCKGPITTFIVEPFVPHNQEYYLS 60
G RGK+G + L +V + + LG ++ + G P+ VE P +E YL
Sbjct: 52 GARGKAGGIKLCRTYNEVRDAAEDLLGKKLVTHQTGPEGKPVQRVYVETADPIERELYLG 111
Query: 61 IVSDRLG--CTISFSECGGIEIEE----NWDKVKTIFLPTEKHMTLDACAPLIATLPLEF 114
V DR + S GG+EIEE + + + + + + L L+
Sbjct: 112 FVLDRKSERVRVIASARGGMEIEEIAAKEPEAIIQVVVEPAVGLQQFQAREIAFGLGLDI 171
Query: 115 R--GKIGDFIMGVFAVFQDLDFSFIEMNPFTLV-NGEPYPLDMRGELDDTAAFK 165
+ + IMG + F+DLD + +E+NP + + LD + DD A F+
Sbjct: 172 KQVSRAVKTIMGCYRAFRDLDATMLEINPLVVTKDDRVLALDAKMSFDDNALFR 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 = 0.40
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 132 LDFSFIEMNPFTLVNGEPYPLDMRGELDDTAAFKNFK---KW 170
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 = 1.7
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 156 GELDDTAAFKNFKKWANIE-------FPLPFGRVLSSTESFIHSLDEKTSASLKFTVLNP 208
E+D ++N K+ + +P F R ++ E D + L+ T+LN
Sbjct: 78 AEVDPRLYYENRSKFIQEQKAKGINPYPHKFERTITVPEFVEKYQDLASGEHLEDTILNV 137
Query: 209 KGRIWTMVAGGGASVIYADTVGDLGYASELGNYA 242
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 = 4.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 9/41 (21%)
Query: 241 YAEYSGAPNEEEVLQYARVVIDCATADPDGRKRALLIGGGI 281
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 = 4.3
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 268 PDGRKRALLIGGGIANFTDVATTFNGI--IRALREKESKLKAAR-MHIFVRRGGPNYQTG 324
D R R + I GGI GI AL E + AR + +F P
Sbjct: 92 DDRRARQIWIAGGI-----------GITPFLALLEALAARGDARPVTLFYCVRDPEDAVF 140
Query: 325 LAKMRALGEELGIPLEV 341
L ++RAL G+ L V
Sbjct: 141 LDELRALAAAAGVVLHV 157
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.8 bits (65), Expect = 5.2
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 203 FTVLNPKGRIWTMVAGGGASVIYADTVG 230
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 = 5.6
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 171 ANIEFPLP-------FGRVLS 184
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 = 8.1
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 208 PKGRIWTMVAGGGASVIYADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDC---- 263
P GR+W G G+++ A GN + P EV +
Sbjct: 438 PAGRLWICTDGNGSTLGVTPEGNVYNLARNDGNNGMLTEGPIRGEVKLFLTGPEGSEFTG 497
Query: 264 ATADPDGR 271
T PDGR
Sbjct: 498 PTFSPDGR 505
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 0.415
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: 19,013,866
Number of extensions: 1905485
Number of successful extensions: 1838
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1819
Number of HSP's successfully gapped: 25
Length of query: 363
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 265
Effective length of database: 6,590,910
Effective search space: 1746591150
Effective search space used: 1746591150
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)