RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2106
(313 letters)
>gnl|CDD|221718 pfam12695, Abhydrolase_5, Alpha/beta hydrolase family. This family
contains a diverse range of alpha/beta hydrolase
enzymes.
Length = 145
Score = 124 bits (312), Expect = 4e-35
Identities = 43/173 (24%), Positives = 68/173 (39%), Gaps = 28/173 (16%)
Query: 107 TIIYSHGNGCDMGQSLATFMDLSARLKCNVLLYDYSGYGSSTGRASEANLYWDIEAVYHT 166
++ HG G D + A A NV+ DY G+G+S G +
Sbjct: 1 LVVLLHGAGGDPE-AYAPLARALASRGYNVVAVDYPGHGASLGAPDAEAVL--------- 50
Query: 167 LRLKYNINCDQIILYGQSIGSVPTVYLASRVNVAGVILHCALLSALRVVFPNFRKSLWFD 226
++ ++I+L G S+G + LA+R + A D
Sbjct: 51 --ADAPLDPERIVLVGHSLGGGVALLLAARDPRVKAAVVLA----------------AGD 92
Query: 227 GLKNIDKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGHN 279
+D L K+ PVL+IHGTRD +V + + P E + + GAGH+
Sbjct: 93 PPDALDDLAKLTVPVLIIHGTRDGVVPPEEAEALAAALPGPAELVVIEGAGHS 145
>gnl|CDD|221720 pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This family
contains alpha/beta hydrolase enzymes of diverse
specificity.
Length = 187
Score = 90.2 bits (224), Expect = 9e-22
Identities = 45/181 (24%), Positives = 69/181 (38%), Gaps = 15/181 (8%)
Query: 108 IIYSHGNGCDMGQSLATFMDLSARLKCNVLLYDYSGYGSSTGRASEANLYWD-IEAVYHT 166
++ HG G +S + A VL D G+G S G D +
Sbjct: 1 VVLLHGAGGS-AESWRPLAEALAA-GYRVLAPDLPGHGDSDGPPRTPYSLEDDAADLAAL 58
Query: 167 LRLKYNINCDQIILYGQSIGSVPTVYLASRV--NVAGVILHCALLSALRVVFPNFRKSL- 223
L + ++L G S+G + A+R VAG++L L L + +L
Sbjct: 59 LD---ALGLGPVVLVGHSLGGAVALAAAARRPERVAGLVLISPPLRDLEELLAADAAALL 115
Query: 224 -----WFDGLKNIDKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGH 278
+ L ++ PVLVIHG D +V + E+ P E + +PGAGH
Sbjct: 116 ALLRAALLDADLREALARLTVPVLVIHGEDDPLVPPEAARRLAEALPG-AELVVLPGAGH 174
Query: 279 N 279
Sbjct: 175 L 175
>gnl|CDD|223999 COG1073, COG1073, Hydrolases of the alpha/beta superfamily [General
function prediction only].
Length = 299
Score = 91.7 bits (227), Expect = 2e-21
Identities = 51/214 (23%), Positives = 78/214 (36%), Gaps = 24/214 (11%)
Query: 107 TIIYSHGN----GCDMGQSLATFMDLSARLKCNVLLYDYSGYGSSTGRASEANLYWDIEA 162
+ G G S A + LS VL DY G+S G A L +
Sbjct: 90 SGGDPRGLADSEGYAEDFSAAVLLLLS----EGVLDKDYRLLGASLGPRILAGLSLGGPS 145
Query: 163 VYHTLRLKYNINC-DQIILYGQSIGSVPTVYLASRVN------VAGVILHCALLSALRVV 215
L +I+++G+S+G + L + +I
Sbjct: 146 AGALLAWGPTRLDASRIVVWGESLGGALALLLLGANPELARELIDYLITPGGFAPLPAPE 205
Query: 216 FPNFRKSLWFDGLKNIDKLP---KIKS-PVLVIHGTRDEIVDFSHGMTIYESCP-NVVEP 270
P L L +D KI PVL++HG RDE+V +YE+ +
Sbjct: 206 APLDTLPLRAVLLLLLDPFDDAEKISPRPVLLVHGERDEVVPLRDAEDLYEAARERPKKL 265
Query: 271 LWVPGAGHNNI----EMFEQYLTRLDKFINEELM 300
L+VPG GH ++ EQ L +L +F+ L+
Sbjct: 266 LFVPGGGHIDLYDNPPAVEQALDKLAEFLERHLL 299
>gnl|CDD|223669 COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta
hydrolase superfamily) [General function prediction
only].
Length = 282
Score = 50.0 bits (118), Expect = 4e-07
Identities = 33/186 (17%), Positives = 57/186 (30%), Gaps = 5/186 (2%)
Query: 115 GCDMGQSLATFMDLSARLKCNVLLYDYSGYGSSTGRASEANLYW--DIEAVYHTLRLKYN 172
G MG ++A + L + L+ A+ + A+ L
Sbjct: 94 GHSMGGAVALALALRHPDRVRGLVLIGPAPPPGLLEAALRQPAGAAPLAALADLLLGLDA 153
Query: 173 INCDQIILYGQSIGSVPTVYLASRVNVAGVILHCALLSALRVVFPNFRKSLWFDGLKNI- 231
++ + ++ A L A +A + L
Sbjct: 154 AAFAALLAALGLLAALAAAARAGLAEALRAPLLGAAAAAFARAARADLAAALLALLDRDL 213
Query: 232 -DKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGHNNIEMF-EQYLT 289
L +I P L+IHG D +V + + PN + +PGAGH E +
Sbjct: 214 RAALARITVPTLIIHGEDDPVVPAELARRLAAALPNDARLVVIPGAGHFPHLEAPEAFAA 273
Query: 290 RLDKFI 295
L F+
Sbjct: 274 ALLAFL 279
Score = 48.5 bits (114), Expect = 2e-06
Identities = 27/140 (19%), Positives = 47/140 (33%), Gaps = 10/140 (7%)
Query: 107 TIIYSHGNGCDMGQSLATFMDLSARLK-CNVLLYDYSGYGSSTGRASEANLYW-DIEAVY 164
++ HG F L A V+ D G+G S + Y D+ A+
Sbjct: 23 PLVLLHGFPGSSSVWRPVFKVLPALAARYRVIAPDLRGHGRSDPAGYSLSAYADDLAALL 82
Query: 165 HTLRLKYNINCDQIILYGQSIGSVPTVYLASR--VNVAGVILHCALLSALRVVFPNFRKS 222
L L ++++L G S+G + LA R V G++L + + +
Sbjct: 83 DALGL------EKVVLVGHSMGGAVALALALRHPDRVRGLVLIGPAPPPGLLEAALRQPA 136
Query: 223 LWFDGLKNIDKLPKIKSPVL 242
D L + +
Sbjct: 137 GAAPLAALADLLLGLDAAAF 156
>gnl|CDD|224423 COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
[Amino acid transport and metabolism].
Length = 620
Score = 50.2 bits (120), Expect = 6e-07
Identities = 43/226 (19%), Positives = 75/226 (33%), Gaps = 45/226 (19%)
Query: 107 TIIYSHG-----NGCDMGQSLATFMDLSARLKCNVLLYDY---SGYGSSTGRASEANLYW 158
I+Y HG G + VL +Y +GYG A +
Sbjct: 396 LIVYIHGGPSAQVGYSFNPEIQVLASAGY----AVLAPNYRGSTGYGREFADAIRGDWGG 451
Query: 159 ----DIEAVYHTLRLKYNINCDQIILYGQSIGSVPTVYLASRVNV--AGVILH--CALLS 210
D+ A L ++ ++I + G S G T+ A++ A V + L
Sbjct: 452 VDLEDLIAAVDALVKLPLVDPERIGITGGSYGGYMTLLAATKTPRFKAAVAVAGGVDWLL 511
Query: 211 ALRVVFPNFRKSLW---FDGLKNIDKL---------PKIKSPVLVIHGTRDEIVDFSHGM 258
R ++ +K IK+P+L+IHG D+ V
Sbjct: 512 YFGESTEGLRFDPEENGGGPPEDREKYEDRSPIFYADNIKTPLLLIHGEEDDRVPIEQAE 571
Query: 259 TIYES-----CPNVVEPLWVPGAGH------NNIEMFEQYLTRLDK 293
+ ++ P VE + P GH N +++ ++ L +
Sbjct: 572 QLVDALKRKGKP--VELVVFPDEGHGFSRPENRVKVLKEILDWFKR 615
>gnl|CDD|225176 COG2267, PldB, Lysophospholipase [Lipid metabolism].
Length = 298
Score = 44.3 bits (105), Expect = 4e-05
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 14/79 (17%)
Query: 231 IDKLPKIKSPVLVIHGTRDEIVDFSHGMT-IYE--SCPNVVEPLWVPGAGHNNIEMF--- 284
+ P I PVL++ G D +VD G+ +E P+ E +PGA H E+
Sbjct: 221 LRDAPAIALPVLLLQGGDDRVVDNVEGLARFFERAGSPD-KELKVIPGAYH---ELLNEP 276
Query: 285 ----EQYLTRLDKFINEEL 299
E+ L + ++ E L
Sbjct: 277 DRAREEVLKDILAWLAEAL 295
>gnl|CDD|217816 pfam03959, FSH1, Serine hydrolase (FSH1). This is a family of
serine hydrolases.
Length = 209
Score = 42.3 bits (100), Expect = 1e-04
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 235 PKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGH 278
P I++P L + G D +V + E+C N L PG GH
Sbjct: 155 PPIQTPSLHVIGELDTVVPEERSEKLAEACKNSATVLEHPG-GH 197
>gnl|CDD|218686 pfam05677, DUF818, Chlamydia CHLPS protein (DUF818). This family
consists of several Chlamydia CHLPS proteins, the
function of which are unknown.
Length = 364
Score = 40.5 bits (95), Expect = 6e-04
Identities = 28/99 (28%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 97 IMIPHNEAVFTIIYSHGNGCDM------GQSLATFMDLSARLKCNVLLYDYSGYGSSTGR 150
I +P ++ S GN + G +++ L+ + N+L+++Y G SSTG
Sbjct: 129 ICLPQAPPDRWMLISLGNSDCLEERAMIGLKKSSWQRLAKLIGANILVFNYPGVMSSTGS 188
Query: 151 ASEANLYWDIEAVYHTLRLKYN-INCDQIILYGQSIGSV 188
+ NL +A LR K QII YG S+G +
Sbjct: 189 ITRENLAKAYQACVRYLRDKEQGPGAKQIIAYGYSLGGL 227
>gnl|CDD|201306 pfam00561, Abhydrolase_1, alpha/beta hydrolase fold. This
catalytic domain is found in a very wide range of
enzymes.
Length = 226
Score = 39.0 bits (91), Expect = 0.001
Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 136 VLLYDYSGYGSSTGRASEANLY-WDIEAVYHTLRLKYNINCDQIILYGQSIGSVPTVYLA 194
V+ +D G+G S+ A+ D+ L + D++ L G S+G + + A
Sbjct: 3 VIAFDLRGFGRSSPPKDFADYRFDDLAEDLEALLDALGL--DKVNLVGHSMGGLIALAYA 60
Query: 195 SRV--NVAGVILHCALLSALR 213
++ V ++L + A
Sbjct: 61 AKYPDRVKALVLVGTVHPAGL 81
>gnl|CDD|216672 pfam01738, DLH, Dienelactone hydrolase family.
Length = 215
Score = 38.5 bits (90), Expect = 0.002
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 231 IDKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCP--NV-VEPLWVPGAGH 278
+D+ P IK+P+L G D V + E+ NV E PGAGH
Sbjct: 136 LDEAPAIKAPILAHFGEEDPFVPAEARDLLEEALRAANVDHELHVYPGAGH 186
>gnl|CDD|215859 pfam00326, Peptidase_S9, Prolyl oligopeptidase family.
Length = 212
Score = 37.6 bits (88), Expect = 0.004
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 224 WFDGLKNIDKLPKIKSPVLVIHGTRDEIVDFSHGMTIY----ESCPNVVEPLWVPGAGH 278
+ D + K P+L+IHG D+ V + + + NV+ L P GH
Sbjct: 130 YLSPYSPYDNV-KAYPPLLLIHGLHDDRVPPAEALKLVAALQAKGKNVLL-LIFPDEGH 186
>gnl|CDD|216940 pfam02230, Abhydrolase_2, Phospholipase/Carboxylesterase. This
family consists of both phospholipases and
carboxylesterases with broad substrate specificity, and
is structurally related to alpha/beta hydrolases
pfam00561.
Length = 213
Score = 37.7 bits (88), Expect = 0.004
Identities = 33/116 (28%), Positives = 46/116 (39%), Gaps = 21/116 (18%)
Query: 169 LKYNINCDQIILYGQSIGSVPTVYLA--SRVNVAGVI-LHCALLSALRVVFPNFRKSLWF 225
LK I +II+ G S G+ +Y A S + G+I AL L FP
Sbjct: 95 LKTGIPASRIIIGGFSQGAAVALYTALTSPQPLGGIIAFSGALP--LPQKFPQ------- 145
Query: 226 DGLKNIDKLPKIKSPVLVIHGTRDEIVDFSHGMTIYE---SCPNVVEPLWVPGAGH 278
+ + I P+L +HG D +V + G E + N V PG GH
Sbjct: 146 ----HPTGVADI--PILQLHGYEDPVVPLALGKLAKEYLKTLLNPVTFKSYPGMGH 195
>gnl|CDD|224561 COG1647, COG1647, Esterase/lipase [General function prediction
only].
Length = 243
Score = 37.7 bits (88), Expect = 0.004
Identities = 38/155 (24%), Positives = 57/155 (36%), Gaps = 38/155 (24%)
Query: 159 DIEAVYHTLRLKYNINCDQIILYGQSIGSVPTVYLASRVNVAGVILHCA---------LL 209
D+E Y L+ D+I + G S+G V + LA ++ CA ++
Sbjct: 71 DVEDGYRDLKEA---GYDEIAVVGLSMGGVFALKLAYHYPPKKIVPMCAPVNVKSWRIII 127
Query: 210 SALRVVFPNFRKSLWFDG------LKNIDKLP-------------------KIKSPVLVI 244
L F N +K D +K+ P KI SP LV+
Sbjct: 128 EGLLEYFRNAKKYEGKDQEQIDKEMKSYKDTPMTTTAQLKKLIKDARRSLDKIYSPTLVV 187
Query: 245 HGTRDEIVDFSHGMTIY-ESCPNVVEPLWVPGAGH 278
G +DE+V IY + E W+ G+GH
Sbjct: 188 QGRQDEMVPAESANFIYDHVESDDKELKWLEGSGH 222
>gnl|CDD|226075 COG3545, COG3545, Predicted esterase of the alpha/beta hydrolase
fold [General function prediction only].
Length = 181
Score = 36.5 bits (85), Expect = 0.006
Identities = 28/134 (20%), Positives = 46/134 (34%), Gaps = 31/134 (23%)
Query: 178 IILYGQSIGSVPTVYLASR--VNVAGVILHCALLSALRVVFPNF--RKSLWFDGLKNIDK 233
++L S+G + A VAG +L V P R + L D
Sbjct: 61 VVLVAHSLGCATVAHWAEHIQRQVAGALL----------VAPPDVSRPEIRPKHLMTFDP 110
Query: 234 LPKIKSP--VLVIHGTRDEIVDFSHGMTIYESCPN-VVEPLWVPGAGHNNIE-------- 282
+P+ P +V+ D V + H + + + +V+ V GH N E
Sbjct: 111 IPREPLPFPSVVVASRNDPYVSYEHAEDLANAWGSALVD---VGEGGHINAESGFGPWPE 167
Query: 283 ---MFEQYLTRLDK 293
+ Q L+R
Sbjct: 168 GYALLAQLLSRATA 181
>gnl|CDD|184875 PRK14875, PRK14875, acetoin dehydrogenase E2 subunit
dihydrolipoyllysine-residue acetyltransferase;
Provisional.
Length = 371
Score = 37.2 bits (87), Expect = 0.008
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 232 DKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGH 278
D+L + PVLVI G +D I+ +H + P+ V +PGAGH
Sbjct: 308 DRLASLAIPVLVIWGEQDRIIPAAHA----QGLPDGVAVHVLPGAGH 350
>gnl|CDD|165193 PHA02857, PHA02857, monoglyceride lipase; Provisional.
Length = 276
Score = 35.2 bits (81), Expect = 0.029
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 233 KLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGHN 279
+PKIK+P+L++ GT +EI D S + E GA H+
Sbjct: 204 IIPKIKTPILILQGTNNEISDVSGAYYFMQHANCNREIKIYEGAKHH 250
>gnl|CDD|202693 pfam03583, LIP, Secretory lipase. These lipases are expressed and
secreted during the infection cycle of these pathogens.
In particular, C. albicans has a large number of
different lipases, possibly reflecting broad lipolytic
activity, which may contribute to the persistence and
virulence of C. albicans in human tissue.
Length = 291
Score = 35.4 bits (82), Expect = 0.029
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 217 PNFRKSLWFDGLKNIDK--LPKIKSPVLVIHGTRDEIVDFSHGMTIYES 263
P K+L +GL DK +P+I PV V HGT DEIV + +Y++
Sbjct: 199 PVINKTLEDNGLLVYDKSAVPQI--PVFVYHGTHDEIVPIADIDALYKN 245
>gnl|CDD|223477 COG0400, COG0400, Predicted esterase [General function prediction
only].
Length = 207
Score = 34.2 bits (79), Expect = 0.047
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 15/91 (16%)
Query: 167 LRLKYNINCDQIILYGQSIGSVPTVYLASRVNVAGVILHCALLSALRVVFPNFRKSLWFD 226
L +Y I+ +IIL G S G+ + L + A+L + + +
Sbjct: 90 LAEEYGIDSSRIILIGFSQGANIALSLGLT---LPGLFAGAILFSGMLPLE-------PE 139
Query: 227 GLKNIDKLPKIKSPVLVIHGTRDEIVDFSHG 257
L ++ P +L+ HGT D +V +
Sbjct: 140 LLPDLAGTP-----ILLSHGTEDPVVPLALA 165
>gnl|CDD|131480 TIGR02427, protocat_pcaD, 3-oxoadipate enol-lactonase. Members of
this family are 3-oxoadipate enol-lactonase. Note that
the substrate is known as 3-oxoadipate enol-lactone,
2-oxo-2,3-dihydrofuran-5-acetate,
4,5-Dihydro-5-oxofuran-2-acetate, and
5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the
catalyzes the fourth step in the protocatechuate
degradation to beta-ketoadipate and then to succinyl-CoA
and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate,
and vanillate all can be converted in one step to
protocatechuate. This enzyme also acts in catechol
degradation. In genomes that catabolize both catechol
and protocatechuate, two forms of this enzyme may be
found. All members of the seed alignment for this model
were chosen from within protocatechuate degradation
operons of at least three genes of the pathway, from
genomes with the complete pathway through
beta-ketoadipate [Energy metabolism, Other].
Length = 251
Score = 34.3 bits (79), Expect = 0.060
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 232 DKLPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGH-NNIEMFEQYLTR 290
D+L I P L I G +D I + P + GAGH +E E +
Sbjct: 187 DRLGAIAVPTLCIAGDQDGSTPPELVREIADLVPGARFAE-IRGAGHIPCVEQPEAFNAA 245
Query: 291 LDKF 294
L F
Sbjct: 246 LRDF 249
>gnl|CDD|225496 COG2945, COG2945, Predicted hydrolase of the alpha/beta superfamily
[General function prediction only].
Length = 210
Score = 32.0 bits (73), Expect = 0.28
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 239 SPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGH 278
SP LVI G D++VD + ES + + +PGA H
Sbjct: 150 SPGLVIQGDADDVVDLVAVLKWQESIK--ITVITIPGADH 187
>gnl|CDD|129513 TIGR00419, tim, triosephosphate isomerase. Triosephosphate
isomerase (tim/TPIA) is the glycolytic enzyme that
catalyzes the reversible interconversion of
glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate. The active site of the enzyme is located
between residues 240-258 of the model
([AV]-Y-E-P-[LIVM]-W-[SA]-I-G-T-[GK]) with E being the
active site residue. There is a slight deviation from
this sequence within the archeal members of this family
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 205
Score = 31.7 bits (72), Expect = 0.35
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 161 EAVYHTLRLKYNINCDQIILYGQSIGSVPTVYLASRVNVAGVILHCALLSA 211
E V+ ++R +N +L G I + LA+++ GV+L L A
Sbjct: 154 EVVHGSVRAVKEVNESVRVLCGAGISTGEDAELAAQLGAEGVLLASGSLKA 204
>gnl|CDD|234315 TIGR03695, menH_SHCHC,
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
synthase. This protein catalyzes the formation of
SHCHC, or (1 R,6
R)-2-succinyl-6-hydroxy-2,
4-cyclohexadiene-1-carboxylate, by elmination of
pyruvate from
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate (SEPHCHC). Note that SHCHC synthase activity
previously was attributed to MenD, which in fact is
SEPHCHC synthase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 252
Score = 31.8 bits (73), Expect = 0.37
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 18/80 (22%)
Query: 222 SLWFDGLKNIDKLPKIKSPVLVIHGTRDEIVDFSH-GMTIYESCPNVVEPLW---VPGAG 277
SLW KL +K PVL + G +DE F + + PN L + AG
Sbjct: 186 SLW-------PKLQALKIPVLYLCGEKDE--KFVQIAKEMQKLIPN----LTLVIIANAG 232
Query: 278 HN-NIEMFEQYLTRLDKFIN 296
HN ++E E + L F+
Sbjct: 233 HNIHLENPEAFAKILLAFLE 252
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 28.8 bits (65), Expect = 0.76
Identities = 13/47 (27%), Positives = 19/47 (40%)
Query: 42 ITQCAFFPPRPASYKIIEHGQKKNKCILKMNQKKHAIISRNVFWTTN 88
I PPR +Y +E Q ++ + K+ K A V W N
Sbjct: 29 IQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVKLAGKKIKVAWAPN 75
>gnl|CDD|226101 COG3571, COG3571, Predicted hydrolase of the alpha/beta-hydrolase
fold [General function prediction only].
Length = 213
Score = 30.2 bits (68), Expect = 0.97
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 234 LPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGHN 279
L +K+P L+ GTRDE S P +E +W+ A H+
Sbjct: 138 LTGLKTPTLITQGTRDEFGTRDEVAGYALSDP--IEVVWLEDADHD 181
>gnl|CDD|223489 COG0412, COG0412, Dienelactone hydrolase and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 236
Score = 30.0 bits (68), Expect = 1.4
Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 22/98 (22%)
Query: 159 DIEAVYHTLRLKYNINCDQIILYGQSIGSVPTVYLASRVNVAGVILHCALLSALRVVFPN 218
DI+A L + ++ +I + G +G G ALL+A R P
Sbjct: 95 DIDAALDYLARQPQVDPKRIGVVGFCMG--------------G---GLALLAATR--APE 135
Query: 219 FRKSL-WFDGLKNIDKL--PKIKSPVLVIHGTRDEIVD 253
+ ++ ++ GL D PKIK PVL+ D +
Sbjct: 136 VKAAVAFYGGLIADDTADAPKIKVPVLLHLAGEDPYIP 173
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 29.6 bits (66), Expect = 1.5
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 176 DQIILYGQSIGSVPTVYLASRVNVAGV--ILHCALLSALRVVFPNFRKSLWFDGLKNIDK 233
+Q L + +G+V V +SR++ V + H L+++R P+ ++S GLK I +
Sbjct: 138 EQGSLLARQLGAVAYVECSSRMSENSVRDVFHVTTLASVRREHPSLKRSTSRRGLKRISQ 197
Query: 234 LP 235
P
Sbjct: 198 QP 199
>gnl|CDD|178419 PLN02824, PLN02824, hydrolase, alpha/beta fold family protein.
Length = 294
Score = 30.1 bits (68), Expect = 1.5
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 234 LPKIKSPVLVIHGTRD--EIVDFSHGMTIYESCPNVVEPLWVPGAGH 278
LP +K PVL+ G +D E V+ Y + V + + +PG GH
Sbjct: 230 LPAVKCPVLIAWGEKDPWEPVELGRA---YANFDAVEDFIVLPGVGH 273
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
family also includes polypyrimidine tract binding
protein homolog 3 (PTBPH3) found in plant. Although its
biological roles remain unclear, PTBPH3 shows
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 27.5 bits (62), Expect = 2.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 16 GIDRITMNLLSFFNLFCCAG 35
G+D+ MN FNLFC G
Sbjct: 6 GLDKDKMNCDKLFNLFCLYG 25
>gnl|CDD|233764 TIGR02177, PorB_KorB, 2-oxoacid:acceptor oxidoreductase, beta
subunit, pyruvate/2-ketoisovalerate family. A number of
anaerobic and microaerophilic species lack pyruvate
dehydrogenase and have instead a four subunit,
oxygen-sensitive pyruvate oxidoreductase, with either
ferredoxins or flavodoxins used as the acceptor. Several
related four-subunit enzymes may exist in the same
species. This model describes a subfamily of beta
subunits, representing mostly pyruvate and
2-ketoisovalerate specific enzymes.
Length = 287
Score = 29.4 bits (66), Expect = 2.5
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 107 TIIYSHGNGCDMGQSLATFMDLSAR-LKCNVLLYDYSGYGSSTGRASEANLYW 158
+I G+G G F+ R + V+++D YG + G+AS L
Sbjct: 73 KVIVVGGDGDLYGIGGNHFVAAGRRNVDITVIVHDNQVYGLTKGQASPTLLKG 125
>gnl|CDD|131155 TIGR02100, glgX_debranch, glycogen debranching enzyme GlgX. This
family consists of the GlgX protein from the E. coli
glycogen operon and probable equivalogs from other
prokaryotic species. GlgX is not required for glycogen
biosynthesis, but instead acts as a debranching enzyme
for glycogen catabolism. This model distinguishes GlgX
from pullanases and other related proteins that also
operate on alpha-1,6-glycosidic linkages. In the wide
band between the trusted and noise cutoffs are
functionally similar enzymes, mostly from plants, that
act similarly but usually are termed isoamylase [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 688
Score = 28.5 bits (64), Expect = 5.4
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 198 NVAGVILHCALLSALRVVFPNFRKSLWFDG 227
++ L ALR P R+ +FDG
Sbjct: 551 GDDELLAFTKKLIALRKAHPVLRRERFFDG 580
>gnl|CDD|215216 PLN02385, PLN02385, hydrolase; alpha/beta fold family protein.
Length = 349
Score = 28.2 bits (63), Expect = 6.4
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 233 KLPKIKSPVLVIHGTRDEIVDFSHGMTIYE 262
+L ++ P+L++HG D++ D S +YE
Sbjct: 274 QLEEVSLPLLILHGEADKVTDPSVSKFLYE 303
>gnl|CDD|215352 PLN02652, PLN02652, hydrolase; alpha/beta fold family protein.
Length = 395
Score = 27.9 bits (62), Expect = 6.6
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 234 LPKIKSPVLVIHGTRDEIVDFSHGMTIYESCPNVVEPLWVPGAGHNNIEMFEQYLTRL 291
+ P +V+HGT D + D +Y + H +I++++ +L L
Sbjct: 320 FKSVTVPFMVLHGTADRVTDPLASQDLYNEAASR----------HKDIKLYDGFLHDL 367
>gnl|CDD|234324 TIGR03712, acc_sec_asp2, accessory Sec system protein Asp2. This
protein is designated Asp2 because, along with SecY2,
SecA2, and other proteins it is part of the accessory
secretory protein system. The system is involved in the
export of serine-rich glycoproteins important for
virulence in a number of Gram-positive species,
including Streptococcus gordonii and Staphylococcus
aureus. This protein family is assigned to transport
rather than glycosylation function, but the specific
molecular role is unknown [Protein fate, Protein and
peptide secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 511
Score = 27.7 bits (62), Expect = 8.7
Identities = 9/29 (31%), Positives = 19/29 (65%)
Query: 176 DQIILYGQSIGSVPTVYLASRVNVAGVIL 204
DQ+IL G S+G+ +Y ++++ +I+
Sbjct: 357 DQLILSGLSMGTFGALYYGAKLSPHAIIV 385
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
0.325 0.139 0.439
Gapped
Lambda K H
0.267 0.0673 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,686,488
Number of extensions: 1471640
Number of successful extensions: 1589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1579
Number of HSP's successfully gapped: 40
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.6 bits)