RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030220
(181 letters)
>gnl|CDD|215066 PLN00125, PLN00125, Succinyl-CoA ligase [GDP-forming] subunit
alpha.
Length = 300
Score = 218 bits (556), Expect = 1e-71
Identities = 105/110 (95%), Positives = 108/110 (98%)
Query: 47 AASHPAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNS 106
A+ PAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFN+
Sbjct: 1 ASPPPAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNT 60
Query: 107 VAEAKAETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
VAEAKAETKANASVIYVPPPFAAAAI+EAMEAELDLVVCITEGIPQHDMV
Sbjct: 61 VAEAKAETKANASVIYVPPPFAAAAILEAMEAELDLVVCITEGIPQHDMV 110
>gnl|CDD|180194 PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha;
Validated.
Length = 291
Score = 212 bits (542), Expect = 1e-69
Identities = 73/105 (69%), Positives = 88/105 (83%)
Query: 52 AVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAK 111
++ ++K+T+VI QGITGK GTFHTEQ + YGT +VGGVTP KGGT LGLPVFN+VAEA
Sbjct: 2 SILINKDTKVIVQGITGKQGTFHTEQMLAYGTNIVGGVTPGKGGTTVLGLPVFNTVAEAV 61
Query: 112 AETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
T ANASVIYVPPPFAA AI+EA++A +DL+VCITEGIP DM+
Sbjct: 62 EATGANASVIYVPPPFAADAILEAIDAGIDLIVCITEGIPVLDML 106
>gnl|CDD|240307 PTZ00187, PTZ00187, succinyl-CoA synthetase alpha subunit;
Provisional.
Length = 317
Score = 211 bits (540), Expect = 6e-69
Identities = 88/127 (69%), Positives = 102/127 (80%), Gaps = 2/127 (1%)
Query: 32 SAAPAAHSRNYGSSAAASHPAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTP 91
AA ++ + ++ S P V+V+KNT+VICQGITGK GTFHTEQAIEYGTKMVGGV P
Sbjct: 3 GAAFMILKVSFRARSSTSAPRVWVNKNTKVICQGITGKQGTFHTEQAIEYGTKMVGGVNP 62
Query: 92 KKGGTEHL--GLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEG 149
KK GT HL GLPVF +V EAK T A+ASVIYVPPP AA+AI+EA+EAE+ LVVCITEG
Sbjct: 63 KKAGTTHLKHGLPVFATVKEAKKATGADASVIYVPPPHAASAIIEAIEAEIPLVVCITEG 122
Query: 150 IPQHDMV 156
IPQHDMV
Sbjct: 123 IPQHDMV 129
>gnl|CDD|223152 COG0074, SucD, Succinyl-CoA synthetase, alpha subunit [Energy
production and conversion].
Length = 293
Score = 192 bits (489), Expect = 1e-61
Identities = 71/105 (67%), Positives = 86/105 (81%)
Query: 52 AVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAK 111
++ ++K+T+VI QGITGK GTFHTEQ + YGTK+VGGVTP KGG LGLPVFN+V EA
Sbjct: 2 SILLNKDTKVIVQGITGKQGTFHTEQMLAYGTKIVGGVTPGKGGQTILGLPVFNTVEEAV 61
Query: 112 AETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
ET ANASVI+VPPPFAA AI+EA++A + LVV ITEGIP DM+
Sbjct: 62 KETGANASVIFVPPPFAADAILEAIDAGIKLVVIITEGIPVLDML 106
>gnl|CDD|130091 TIGR01019, sucCoAalpha, succinyl-CoA synthetase, alpha subunit.
This model describes succinyl-CoA synthetase alpha
subunits but does not discriminate between GTP-specific
and ATP-specific reactions. The model is designated as
subfamily rather than equivalog for that reason. ATP
citrate lyases appear to form an outgroup [Energy
metabolism, TCA cycle].
Length = 286
Score = 189 bits (483), Expect = 8e-61
Identities = 70/104 (67%), Positives = 85/104 (81%)
Query: 53 VFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKA 112
+ +DK+T+VI QGITG G+FHTEQ + YGT +VGGVTP KGGT LGLPVF+SV EA
Sbjct: 1 ILLDKDTKVIVQGITGSQGSFHTEQMLAYGTNIVGGVTPGKGGTTVLGLPVFDSVKEAVE 60
Query: 113 ETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
ET ANASVI+VP PFAA AI EA++A ++L+VCITEGIP HDM+
Sbjct: 61 ETGANASVIFVPAPFAADAIFEAIDAGIELIVCITEGIPVHDML 104
>gnl|CDD|202320 pfam02629, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 96
Score = 129 bits (327), Expect = 2e-39
Identities = 44/96 (45%), Positives = 59/96 (61%), Gaps = 2/96 (2%)
Query: 56 DKNTRVICQGITGKN--GTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKAE 113
DK+T+V G G G +H Q + YG KMV GV P+KGGTE G+PV+ SV E + +
Sbjct: 1 DKDTKVAVIGAGGLGIQGLYHFIQLLGYGIKMVFGVNPRKGGTEVGGIPVYKSVDELEED 60
Query: 114 TKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEG 149
T + +VI VP PFA AI E ++A + +V IT G
Sbjct: 61 TGVDVAVITVPAPFAQEAIDELVDAGIKGIVNITPG 96
>gnl|CDD|214881 smart00881, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 100
Score = 120 bits (303), Expect = 6e-36
Identities = 46/100 (46%), Positives = 60/100 (60%), Gaps = 3/100 (3%)
Query: 54 FVDKNTRVICQGITGKNGTFHTEQAI---EYGTKMVGGVTPKKGGTEHLGLPVFNSVAEA 110
++ NT V G +G G+F EYGTK VGGV P K G + G+PV++SVAEA
Sbjct: 1 LLNPNTSVAVVGASGNLGSFGLAVMRNLLEYGTKFVGGVYPGKVGPKVDGVPVYDSVAEA 60
Query: 111 KAETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGI 150
ET + +VI+VP A AI EA+EA + +V ITEGI
Sbjct: 61 PEETGVDVAVIFVPAEAAPDAIDEAIEAGIKGIVVITEGI 100
>gnl|CDD|178137 PLN02522, PLN02522, ATP citrate (pro-S)-lyase.
Length = 608
Score = 37.5 bits (87), Expect = 0.002
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 95 GTEHLGLPVFNSVAEA-KAETKANASVIYVPPPFAAAAIMEAMEAE-LDLVVCITEGIPQ 152
G E + +PV S+ A KA A+ + + AAA+ MEA++ + +V I EG+P+
Sbjct: 57 GQEEIAIPVHGSIEAACKAHPTADVFINFASFRSAAASSMEALKQPTIRVVAIIAEGVPE 116
Query: 153 HDM--VINFTRVN 163
D +I + R N
Sbjct: 117 SDTKQLIAYARAN 129
>gnl|CDD|236451 PRK09284, PRK09284, thiamine biosynthesis protein ThiC;
Provisional.
Length = 607
Score = 32.9 bits (76), Expect = 0.067
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 81 YGTKMVGGVTPKKGGTEHLGLP 102
+GT M+ VTPK EHLGLP
Sbjct: 470 FGTAMLCYVTPK----EHLGLP 487
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 31.4 bits (71), Expect = 0.22
Identities = 31/129 (24%), Positives = 45/129 (34%), Gaps = 22/129 (17%)
Query: 44 SSAAASHPAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPV 103
A AS K V G TG+ G EQ + G + GV
Sbjct: 3 EGAEASEEDAENVKTKTVFVAGATGRTGKRIVEQLLAKGFAVKAGVR------------- 49
Query: 104 FNSVAEAKAETKANASVIYVPPPFAAAA--IMEAMEAELDLVVCITEGIPQHDM-----V 156
V +AK + S+ V + ++EA+ + D V+C T D V
Sbjct: 50 --DVDKAKTSLPQDPSLQIVRADVTEGSDKLVEAIGDDSDAVICATGFRRSFDPFAPWKV 107
Query: 157 INFTRVNIL 165
NF VN++
Sbjct: 108 DNFGTVNLV 116
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 31.2 bits (71), Expect = 0.31
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 79 IEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEAMEA 138
+EYG + V PK E LG+ + SVA+ + +VI VP + E E
Sbjct: 34 LEYGQGKIYPVNPKYD--EVLGVKAYTSVADLPDA--PDLAVIVVPAKVVPEIVHELGEK 89
Query: 139 ELDLVVCITEGI 150
+ + I+ G
Sbjct: 90 GVKGAIVISAGF 101
>gnl|CDD|149039 pfam07755, DUF1611, Protein of unknown function (DUF1611). This
region is found in a number of hypothetical bacterial
and archaeal proteins. The region is approximately 350
residues long. A member of this family is thought to
associate with another subunit to form an
H+-transporting ATPase, but no evidence has been found
to support this.
Length = 302
Score = 30.6 bits (70), Expect = 0.43
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 98 HLGLPVFNSVAEAKAETKANASVIYVP--------PPFAAAAIMEAMEAELDLV 143
G+P+ +S+ EA A A A + + P ++EA+EA LD+V
Sbjct: 17 GRGIPIVSSLEEALA---AGADTLIIGIAPSGGVLPEAWREVLLEALEAGLDVV 67
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 29.1 bits (66), Expect = 0.56
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 67 TGKNGTFHTEQAIEY--GTKMVGGVTPKKGGTE----HLGLPVFNSVAEAKAETKANASV 120
GK G H E G ++VG + P E G+P ++ + E A+ +A
Sbjct: 8 AGKIGRRHLRALNESQDGAELVGILDPDPARAEAVAESFGVPAYSDLEELLADPDIDAVS 67
Query: 121 IYVPPPFAAAAIMEAMEAELDLVV 144
+ PP + A+EA ++
Sbjct: 68 VATPPGLHFELALAALEAGKHVLC 91
>gnl|CDD|225902 COG3367, COG3367, Uncharacterized conserved protein [Function
unknown].
Length = 339
Score = 29.3 bits (66), Expect = 1.00
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 65 GITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVIYVP 124
G+ + + ++ TP++ G + +P+ +SV EA E A A +I +
Sbjct: 20 GLLRYSEKYAIVAVVDRREAGD--DTPRELGGDKADVPIISSVEEAL-EGLAEALIIGIA 76
Query: 125 PPFAA------AAIMEAMEAELDLV 143
PP I+EA+EA +++V
Sbjct: 77 PPGGVLPESWREYIVEALEAGMNVV 101
>gnl|CDD|224997 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy
production and conversion].
Length = 260
Score = 28.8 bits (65), Expect = 1.5
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 20/80 (25%)
Query: 76 EQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVI-----YVPPPFAAA 130
+QAI+ T VG + E LG P V++ + +V +
Sbjct: 119 KQAIDGDTGQVGPLL-----AELLGWPQVTYVSKIEIVDGGKVTVERELEGGL------- 166
Query: 131 AIMEAMEAELDLVVCITEGI 150
E +EA L VV + I
Sbjct: 167 ---ETVEAPLPAVVTVDLRI 183
>gnl|CDD|129294 TIGR00190, thiC, thiamine biosynthesis protein ThiC. The thiC
ortholog is designated thiA in Bacillus subtilis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 423
Score = 28.9 bits (65), Expect = 1.7
Identities = 14/41 (34%), Positives = 15/41 (36%), Gaps = 4/41 (9%)
Query: 81 YGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVI 121
G + VTPK EHL LP V E K A
Sbjct: 317 AGADFLCYVTPK----EHLALPNVEDVKEGVIAYKIAAHAA 353
>gnl|CDD|131764 TIGR02717, AcCoA-syn-alpha, acetyl coenzyme A synthetase (ADP
forming), alpha domain. Although technically
reversible, it is believed that this group of
ADP-dependent acetyl-CoA synthetases (ACS) act in the
direction of acetate and ATP production in the organisms
in which it has been characterized. In most species this
protein exists as a fused alpha-beta domain polypeptide.
In Pyrococcus and related species, however the domains
exist as separate polypeptides. This model represents
the alpha (N-terminal) domain. In Pyrococcus and related
species there appears to have been the development of a
paralogous family such that four other proteins are
close relatives. In reference , one of these (along with
its beta-domain partner) was characterized as ACS-II
showing specificity for phenylacetyl-CoA. This model has
been constructed to exclude these non-ACS-I paralogs.
This may result in new, authentic ACS-I sequences
falling below the trusted cutoff.
Length = 447
Score = 28.4 bits (64), Expect = 2.4
Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 79 IEYGTK-MVGGVTPKKGGTEHLGLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEAME 137
IE G K + V PK G E LG+ + SV E + +VI VP + + E E
Sbjct: 31 IEGGYKGKIYPVNPKAG--EILGVKAYPSVLEIPDPV--DLAVIVVPAKYVPQVVEECGE 86
Query: 138 AELDLVVCITEG 149
+ V IT G
Sbjct: 87 KGVKGAVVITAG 98
>gnl|CDD|218666 pfam05633, DUF793, Protein of unknown function (DUF793). This
family consists of several plant proteins of unknown
function.
Length = 389
Score = 28.3 bits (63), Expect = 2.4
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 2 ARQALAKLIGSIGSRRPSTASSVSHYRLSSSAAPAAHSRNYGSSAAAS 49
A++AL L + + S S H S + + H R+ GSS +
Sbjct: 156 AKKALTDLAIGMLDEKDSGGSGGGHRNRSFGRSWSFHHRSIGSSGGGT 203
>gnl|CDD|223499 COG0422, ThiC, Thiamine biosynthesis protein ThiC [Coenzyme
metabolism].
Length = 432
Score = 28.4 bits (64), Expect = 2.4
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 4/22 (18%)
Query: 81 YGTKMVGGVTPKKGGTEHLGLP 102
G M+ VTP EHLGLP
Sbjct: 318 AGADMLCYVTPA----EHLGLP 335
>gnl|CDD|226721 COG4271, COG4271, Predicted nucleotide-binding protein containing
TIR -like domain [Transcription].
Length = 233
Score = 27.6 bits (61), Expect = 3.4
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 97 EHLGLPVFNSVAEA--KAETKANASVIYVPPPF--AAAAIMEAMEAELDLVVCITEGIP 151
+ LG+ N+ A A A T N ++V A A +EA+ + L I +G+
Sbjct: 59 KCLGVQPANAAAPAPQNAATMPNLKKVFVVSGHDAIARAELEALLRDWKLEPVILDGLF 117
>gnl|CDD|200538 cd11277, Sema_plexin_B3, The Sema domain, a protein interacting
module, of Plexin B3. Plexin B3 is the receptor of
semaphorin 5A. It is a highly potent stimulator of
neurite outgrowth of primary murine cerebellar neurons.
Plexin B3 has been linked to verbal performance and
white matter volume in human brain. Furthermore, Sema5A
and plexin B3 have been implicated in the progression of
various types of cancer. They play an important role in
the invasion and metastasis of gastric carcinoma. The
stimulation of plexin B3 by Sema5A binding in human
glioma cells results in the inhibition of cell migration
and invasion. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 434
Score = 27.5 bits (61), Expect = 4.3
Identities = 26/113 (23%), Positives = 39/113 (34%), Gaps = 14/113 (12%)
Query: 32 SAAPAAHSRNYGSSAAASHPAVFVDK---NTRVICQGITGKNGTFHTEQAIEYGTKMVGG 88
+A + +A ++P V +D R +C G E IEYG
Sbjct: 261 AAGQGSTPTPTDQTALCAYPLVELDSAMERARRLCYTAGGGGPNGKEEATIEYGVTSRCV 320
Query: 89 VTPKKG------GTEHLGLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEA 135
PK G EH P+ ++ +A + PP A AA+ E
Sbjct: 321 NLPKDSPESYPCGDEHTPSPI-----ASRQPLEAEPLLTLTPPLTAVAALQED 368
>gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl
reductase.
Length = 390
Score = 27.4 bits (61), Expect = 4.9
Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 10/98 (10%)
Query: 5 ALAKLIGSIGSRRPSTASSVSHYRLSSSAAPAAHSRNYGSSAAASHPAVFVD-------- 56
L+ + S+ + +++S + RL++S A R +S + A
Sbjct: 1 HLSSSLFSLRAAAAASSSPSN--RLAASLGGALVRRAAAASRGSRATAAAAAQSFRSKEP 58
Query: 57 KNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKG 94
K+ V+ G TG G F + + G +V K G
Sbjct: 59 KDVTVLVVGATGYIGKFVVRELVRRGYNVVAVAREKSG 96
>gnl|CDD|216813 pfam01964, ThiC, ThiC family. ThiC is found within the thiamine
biosynthesis operon. ThiC is involved in pyrimidine
biosynthesis. The precise catalytic function of ThiC is
still not known. ThiC participates in the formation of
4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an
intermediate in the de novo pyrimidine biosynthesis.
Length = 421
Score = 27.0 bits (61), Expect = 5.6
Identities = 10/22 (45%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 81 YGTKMVGGVTPKKGGTEHLGLP 102
G + VTP EHLGLP
Sbjct: 316 AGADFLCYVTPA----EHLGLP 333
>gnl|CDD|226208 COG3683, COG3683, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 213
Score = 26.6 bits (59), Expect = 7.0
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 43 GSSAAASHPAVFVDKNTRVICQ 64
S A +HP VF+D T V+ +
Sbjct: 17 ISILAYAHPHVFIDARTEVVIE 38
>gnl|CDD|233459 TIGR01541, tape_meas_lam_C, phage tail tape measure protein, lambda
family. This model represents a relatively
well-conserved region near the C-terminus of the tape
measure protein of a lambda and related phage. This
protein, which controls phage tail length, is typically
about 1000 residues in length. Both low-complexity
sequence and insertion/deletion events appear common in
this family. Mutational studies suggest a ruler or
template role in the determination of phage tail length.
Similar behavior is attributed to proteins from
distantly related or unrelated families in other phage
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 332
Score = 26.3 bits (58), Expect = 8.9
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 11/66 (16%)
Query: 1 MARQALAKLIGSIGSRRPSTAS---SVSHYRLSSSAAPAAHSRNYGSSAAAS-------- 49
+A+ A+A L SIGS S S S S AA + G +A
Sbjct: 212 IAKLAIAGLAQSIGSLFGGAVSGGASSSGAMASYGAAYVFNFAGGGYTAGGGKYEPSGVV 271
Query: 50 HPAVFV 55
HP FV
Sbjct: 272 HPGEFV 277
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
0.318 0.130 0.372
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,003,841
Number of extensions: 809095
Number of successful extensions: 792
Number of sequences better than 10.0: 1
Number of HSP's gapped: 787
Number of HSP's successfully gapped: 34
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)