RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7666
(350 letters)
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 129 bits (327), Expect = 5e-34
Identities = 66/250 (26%), Positives = 114/250 (45%), Gaps = 28/250 (11%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPITS 156
+TL E+ R+GG +R+V +G +FE+GP + L L+++LGL D+++
Sbjct: 28 VTLFEADDRVGGLLRTV-KIDGFLFERGPHHFLARKEE---ILDLIKELGLEDKLL---- 79
Query: 157 SHPTAQNRLIYVNKKLHKLPSNFFSLFKTHSPFSKPLIFSILHDLTTK--TVPKSDESIY 214
+ + IY + KLH +P+ S+ + L + PK D S+
Sbjct: 80 -WNSTARKYIYYDGKLHPIPTPTILGIPLLLLSSEAGLARALQEFIRPKSWEPKQDISVG 138
Query: 215 DFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGAIKEMMS 274
+F+ RRFG EV + + ++ GI AGDA K+S L E+ +G +++GA KE +
Sbjct: 139 EFIRRRFGEEVVERFIEPLLEGIYAGDADKLSAAAAFPILARAERKYGSLLRGAKKEGLP 198
Query: 275 KRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNKVEVKMDTTCTNLEFL 334
K+ + GGLQ+++ L E L + +++ T T ++
Sbjct: 199 KQSLKKEK----FG-----------YLRGGLQSLIEALAEKL--EAKIRTGTEVTKIDKK 241
Query: 335 EKGVKAVDQP 344
G VD
Sbjct: 242 GAGKTIVDVG 251
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 117 bits (296), Expect = 1e-29
Identities = 73/263 (27%), Positives = 119/263 (45%), Gaps = 51/263 (19%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGA--NTLKLVEDLGLADQVIPI 154
ITLLE+S RLGG +++V +G E GP + L + LV++LGL D+++
Sbjct: 28 ITLLEASDRLGGKIQTV-RKDGFPIELGP-----ESFLARKPSAPALVKELGLEDELV-- 79
Query: 155 TSSHPTAQNRLIYVNKKLHKLPSNFFSLFKTHSPFS-KPLIFSILHDLTTK--------- 204
++ T Q+ IYVN KLH +P ++ P S P +F+ L K
Sbjct: 80 ANT--TGQS-YIYVNGKLHPIPPG--TVMGI--PTSIAPFLFAGLVSPIGKLRAAADLRP 132
Query: 205 --TVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMA---KLFELEQ 259
P D+S+ F RRFG EV + + ++ GI AGD +S L A +L + E
Sbjct: 133 PRWKPGQDQSVGAFFRRRFGDEVVENLIEPLLSGIYAGDIDTLS---LRATFPQLAQAED 189
Query: 260 LHGGVIKGAIKEMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNK 319
+G +++G K + ++ G +++GGLQ+++ L E L
Sbjct: 190 KYGSLLRGMRKALPKEKKKTKGV---------------FGTLKGGLQSLIEALEEKLPAG 234
Query: 320 VEVKMDTTCTNLEFLEKGVKAVD 342
+ T T ++ G + V
Sbjct: 235 -TIHKGTPVTKIDKSGDGYEIVL 256
>gnl|CDD|215314 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 111 bits (280), Expect = 3e-27
Identities = 68/247 (27%), Positives = 109/247 (44%), Gaps = 22/247 (8%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLAD-QVIPIT 155
+ + E+ R+GG + SV +G I+E+GP + +P L D GL D V P
Sbjct: 39 VLVTEARDRVGGNITSVSE-DGFIWEEGPNSFQP----SDPELTSAVDSGLRDDLVFPDP 93
Query: 156 SSHPTAQNRLIYVNKKLHKLPSN-----FFSLFKTHSPFSKPLIFSILHDLTTKTVPKSD 210
+ R + N KL LPSN F L + + + P +
Sbjct: 94 QA-----PRYVVWNGKLRPLPSNPIDLPTFDLLSAPGKI-RAGLGAFG--WKRPPPPGRE 145
Query: 211 ESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGAIK 270
ES+ +FV R G EV + + + G+ AGD +S+ KL+ LE+ G +I GAIK
Sbjct: 146 ESVGEFVRRHLGDEVFERLIDPFVSGVYAGDPSSLSMKAAFPKLWNLEKRGGSIIGGAIK 205
Query: 271 EMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNKVEVKMDTTCTN 330
+ + + R + + +V S GGLQT+ + L + L K +VK++ +
Sbjct: 206 AIQEAKKNPKPEPRDP--RLPKPKGQTVGSFRGGLQTLPDALAKRLG-KDKVKLNWKVLS 262
Query: 331 LEFLEKG 337
L + G
Sbjct: 263 LSKNDDG 269
>gnl|CDD|213540 TIGR00562, proto_IX_ox, protoporphyrinogen oxidase. This enzyme
oxidizes protoporphyrinogen IX to protoporphyrin IX, a
precursor of heme and chlorophyll. Bacillus subtilis
HemY also has coproporphyrinogen III to coproporphyrin
III oxidase activity in a heterologous expression
system, although the role for this activity in vivo is
unclear. This protein is a flavoprotein and has a
beta-alpha-beta dinucleotide binding motif near the
amino end [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 462
Score = 101 bits (252), Expect = 1e-23
Identities = 71/265 (26%), Positives = 122/265 (46%), Gaps = 41/265 (15%)
Query: 87 LCTVLRIST-------PITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTL 139
LC + +TL+E+S R+GG +++V+ +G + E+GP + + + +
Sbjct: 15 LCAAYYLEKEIPELPVELTLVEASDRVGGKIQTVKE-DGYLIERGPDSFLERKK---SAP 70
Query: 140 KLVEDLGLADQVIPITSSHPTAQNRLIYVNK-KLHKLPSNFFSLFKTHSPFSKPLIFSI- 197
LV+DLGL + S T Q R + VN+ KL +P+ +PF K +FS+
Sbjct: 71 DLVKDLGLE----HVLVSDATGQ-RYVLVNRGKLMPVPTKI-------APFVKTGLFSLG 118
Query: 198 -----LHDLTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMA 252
D P DES+ +FV RRFG EV + + ++ GI AGD K+S+
Sbjct: 119 GKLRAGMDFIRPASPGKDESVEEFVRRRFGDEVVENLIEPLLSGIYAGDPSKLSLKSTFP 178
Query: 253 KLFELEQLHGGVIKGAIKEMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTL 312
K ++ EQ HG +I G M K + + S L ++ + ++ GL+T+
Sbjct: 179 KFYQTEQKHGSLILG-----MKKTR--NLPQGSGLQLTAKKQGQDFQTLATGLETLP--- 228
Query: 313 GEHLSNKVEVKMDTTCTNLEFLEKG 337
E + ++++ T + L
Sbjct: 229 -EEIEKRLKLTKVYKGTKVTKLSHR 252
>gnl|CDD|183516 PRK12416, PRK12416, protoporphyrinogen oxidase; Provisional.
Length = 463
Score = 61.0 bits (148), Expect = 3e-10
Identities = 61/250 (24%), Positives = 110/250 (44%), Gaps = 35/250 (14%)
Query: 92 RISTPITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQV 151
I + L+E LGG + SV+ + I E G +I + + + LV+DL L +++
Sbjct: 28 NIDLNLILVEKEEYLGGKIHSVEEKD-FIMESGADSIVARNE---HVMPLVKDLNLEEEM 83
Query: 152 IPITSSHPTAQNRLIYVNKKLHKLPSNFF--------SLFKTHSPFSKPLIFSILHDLTT 203
+ + IY + LH +PS+ SLF + +K I + L D T
Sbjct: 84 V-----YNETGISYIYSDNTLHPIPSDTIFGIPMSVESLFSSTLVSTKGKIVA-LKDFIT 137
Query: 204 K-TVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHG 262
K D S+ F+ G E+ + ++ ++ G+ +G ++++ + L + + +G
Sbjct: 138 KNKEFTKDTSLALFLESFLGKELVERQIAPVLSGVYSGKLNELTMASTLPYLLDYKNKYG 197
Query: 263 GVIKGAIKEMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNKVEV 322
+IK G+EE++ +S K V S +GGL TI++ L E L+ V
Sbjct: 198 SIIK--------------GFEENKKQFQSAGNKKFV-SFKGGLSTIIDRLEEVLTE-TVV 241
Query: 323 KMDTTCTNLE 332
K T +
Sbjct: 242 KKGAVTTAVS 251
>gnl|CDD|216593 pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase.
This family consists of various amine oxidases,
including maze polyamine oxidase (PAO) and various
flavin containing monoamine oxidases (MAO). The aligned
region includes the flavin binding site of these
enzymes. The family also contains phytoene
dehydrogenases and related enzymes. In vertebrates MAO
plays an important role regulating the intracellular
levels of amines via there oxidation; these include
various neurotransmitters, neurotoxins and trace amines.
In lower eukaryotes such as aspergillus and in bacteria
the main role of amine oxidases is to provide a source
of ammonium. PAOs in plants, bacteria and protozoa
oxidase spermidine and spermine to an aminobutyral,
diaminopropane and hydrogen peroxide and are involved in
the catabolism of polyamines. Other members of this
family include tryptophan 2-monooxygenase, putrescine
oxidase, corticosteroid binding proteins and
antibacterial glycoproteins.
Length = 444
Score = 46.4 bits (110), Expect = 1e-05
Identities = 41/253 (16%), Positives = 84/253 (33%), Gaps = 35/253 (13%)
Query: 96 PITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPIT 155
+T+LE+ R+GG +R+V+ +G + E G + N L L+ +LGL
Sbjct: 16 DVTVLEARDRVGGRIRTVRF-DGFLIELGAQWFHGA---YPNLLNLLLELGLEL------ 65
Query: 156 SSHPTAQNRLIYVNKKLHKLPSNFFSLFKTHSPFSKPLIFSILHDLTTKTVPKSDESIYD 215
+ ++ P L+ ++ + + S+ +
Sbjct: 66 -GLLLFPFPGDPFVRLKYRGGPYPD--LPGDLPPPLFLLLR--------SLLELELSLEE 114
Query: 216 FVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLH--GGVIKGAIKEMM 273
+ R VA ++ + + + L A F L ++ GA+ +
Sbjct: 115 PIRRALLLLVALLLLAPELLELDLLSFS----DLLSAAGFLELFLLLFRSLLAGALGFLP 170
Query: 274 SKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSN-----KVEVKMDTTC 328
+LS R +E V GG + L + ++ V+++T
Sbjct: 171 ---LELSARLALLSLRLFDLEDGGVVFPGGGFTLPLGGLPQLIAAALGLLGGRVRLNTRV 227
Query: 329 TNLEFLEKGVKAV 341
++ GV
Sbjct: 228 RSITKSGDGVTVT 240
>gnl|CDD|205628 pfam13450, NAD_binding_8, NAD(P)-binding Rossmann-like domain.
Length = 66
Score = 34.8 bits (81), Expect = 0.005
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDL 145
+ +LE R+GG S + P G + G N +L+++L
Sbjct: 22 VLVLEKRDRIGGNAYSERDP-GYRHDYGAHIFHTSYP---NVRELLDEL 66
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 33.9 bits (78), Expect = 0.11
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 119 LIFEKGPRTIRPKGR---LGANTLKLVEDLGLADQV 151
+ E+ PR + +GR L N L+ +E LGL D++
Sbjct: 29 TLLERAPRELLERGRGIALSPNALRALERLGLWDRL 64
>gnl|CDD|225885 COG3349, COG3349, Uncharacterized conserved protein [Function
unknown].
Length = 485
Score = 33.9 bits (78), Expect = 0.12
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKG 124
+TL E+ RLGG V S + +G E G
Sbjct: 26 VTLYEARDRLGGKVASWRDSDGNHVEHG 53
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 32.1 bits (73), Expect = 0.39
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 14/82 (17%)
Query: 193 LIFSILHDLTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMA 252
L FSIL D V D R S +++ A +S I G+C G A +
Sbjct: 120 LAFSILSDAPMPEVSDRD---------RI-SMISELASASGIAGMCGGQALDLEAEGKQV 169
Query: 253 KLFELEQLH----GGVIKGAIK 270
L LE++H G +I+ A++
Sbjct: 170 PLDALERIHRHKTGALIRAAVR 191
>gnl|CDD|215091 PLN00179, PLN00179, acyl- [acyl-carrier protein] desaturase.
Length = 390
Score = 30.8 bits (70), Expect = 1.2
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 234 ICGICAGDAKK--ISVNFLMAKLFELEQLHGGVIKGAIKEMMSKR 276
ICG A D K+ + ++ KLFE++ G V+ A +MM K+
Sbjct: 246 ICGTIAADEKRHETAYTRIVEKLFEIDP-DGAVL--AFADMMRKK 287
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 30.3 bits (69), Expect = 1.4
Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 15/82 (18%)
Query: 239 AGDAKKISVNFL-MAKLFELEQLHGGVIKGAIKEMMSKRPDLSGYEESELYRRSRI---- 293
AG+A ++L + E L+ EM+++ DL +R +
Sbjct: 163 AGEA-----SYLPQDYVTEDPLLNPDEYTRLYAEMVAEFGDLIEVRAG--WRSQGLPLFV 215
Query: 294 ---EKWSVWSVEGGLQTIVNTL 312
+K S W + GL++++ T
Sbjct: 216 RMMDKDSSWGGDNGLKSLIPTA 237
>gnl|CDD|235977 PRK07233, PRK07233, hypothetical protein; Provisional.
Length = 434
Score = 29.9 bits (68), Expect = 1.9
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 26/88 (29%)
Query: 96 PITLLESSSRLGGWVRSVQSPEGLIFEK-------GPRTIRPKGRLGANTLKLVEDLGLA 148
+T+ E+ +LGG S + GL E+ + L+L+++LGL
Sbjct: 24 EVTVFEADDQLGGLAASFEF-GGLPIERFYHHIFKSDEAL----------LELLDELGLE 72
Query: 149 DQVI-PITSSHPTAQNRLIYVNKKLHKL 175
D++ T T YV+ KL+ L
Sbjct: 73 DKLRWRETK---TGY----YVDGKLYPL 93
>gnl|CDD|233555 TIGR01740, pyrF, orotidine 5'-phosphate decarboxylase, subfamily 1.
This model represents orotidine 5'-monophosphate
decarboxylase, the PyrF protein of pyrimidine nucleotide
biosynthesis. In many eukaryotes, the region hit by this
model is part of a multifunctional protein [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 214
Score = 28.9 bits (65), Expect = 3.2
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 87 LCTVLRISTPITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLG 146
L L ++T L+ + LG + ++ L+ + G + I +L + DL
Sbjct: 1 LIVALDVTTKEEALDLADSLGEEICVIKVGIDLLLDGGEKIIDELAKLNK---LIFLDLK 57
Query: 147 LADQVIPITSS 157
AD IP T
Sbjct: 58 FAD--IPNTVK 66
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.9 bits (65), Expect = 4.1
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 276 RPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLS 317
RPD + E R + W + ++ GL T++ G LS
Sbjct: 433 RPDATDEELWAALERVGLADW-LRALPDGLDTVLGEGGARLS 473
>gnl|CDD|234221 TIGR03467, HpnE, squalene-associated FAD-dependent desaturase. The
sequences in this family are members of the pfam01593
superfamily of flavin-containing amine oxidases which
include the phytoene desaturases. These sequences also
include a FAD-dependent oxidoreductase domain,
pfam01266. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of squalene, the
condensation product of the polyisoprenoid farnesyl
pyrophosphate. This gene and its association with hopene
biosynthesis in Zymomonas mobilis has been noted in the
literature where the gene symbol hpnE was assigned. This
gene is also found in contexts where the downstream
conversion of squalene to hopenes is not evidence. The
precise nature of the reaction catalyzed by this enzyme
is unknown at this time.
Length = 411
Score = 28.9 bits (65), Expect = 4.4
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 96 PITLLESSSRLGGWVRSVQSPE-GLIFEKGPRTIRPKGRLGANT--LKLVEDLGLAD 149
+TL E+ RLGG RS + G + G + LGA T L L+ +G
Sbjct: 4 RVTLFEARPRLGGRARSFEDGGLGQTIDNGQHVL-----LGAYTNLLALLRRIGAEP 55
>gnl|CDD|235205 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E;
Validated.
Length = 630
Score = 28.2 bits (64), Expect = 8.0
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 219 RRFGSEVADYA 229
RR G+E+ADYA
Sbjct: 326 RRLGTELADYA 336
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 0.135 0.393
Gapped
Lambda K H
0.267 0.0851 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,366,014
Number of extensions: 1643991
Number of successful extensions: 1331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1313
Number of HSP's successfully gapped: 21
Length of query: 350
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 252
Effective length of database: 6,590,910
Effective search space: 1660909320
Effective search space used: 1660909320
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 (26.3 bits)