RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4131
(241 letters)
>gnl|CDD|216574 pfam01565, FAD_binding_4, FAD binding domain. This family consists
of various enzymes that use FAD as a co-factor, most of
the enzymes are similar to oxygen oxidoreductase. One of
the enzymes Vanillyl-alcohol oxidase (VAO) has a solved
structure, the alignment includes the FAD binding site,
called the PP-loop, between residues 99-110. The FAD
molecule is covalently bound in the known structure,
however the residue that links to the FAD is not in the
alignment. VAO catalyzes the oxidation of a wide variety
of substrates, ranging form aromatic amines to
4-alkylphenols. Other members of this family include
D-lactate dehydrogenase, this enzyme catalyzes the
conversion of D-lactate to pyruvate using FAD as a
co-factor; mitomycin radical oxidase, this enzyme
oxidises the reduced form of mitomycins and is involved
in mitomycin resistance. This family includes MurB an
UDP-N-acetylenolpyruvoylglucosamine reductase enzyme
EC:1.1.1.158. This enzyme is involved in the
biosynthesis of peptidoglycan.
Length = 139
Score = 91.9 bits (229), Expect = 2e-23
Identities = 30/88 (34%), Positives = 47/88 (53%)
Query: 131 IRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRAS 190
+ R+N IL +D ++ A +EAG+ DL R L ++G G EP S ++GG +AT
Sbjct: 50 LSRLNGILEIDPEDGTATVEAGVTLGDLVRALAAKGLLLGLEPGSGIPGTVGGAIATNGG 109
Query: 191 GMKKNLYGNIEDLLVQVTMVTARGTLER 218
G YG D ++ + +V A G + R
Sbjct: 110 GYGSERYGLTRDNVLSLEVVLADGEVVR 137
>gnl|CDD|223354 COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production
and conversion].
Length = 459
Score = 88.0 bits (218), Expect = 4e-20
Identities = 34/109 (31%), Positives = 58/109 (53%), Gaps = 1/109 (0%)
Query: 132 RRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASG 191
R+N IL +D ++ A ++AG+ +DLE+ L G +P S +++GG +AT A G
Sbjct: 82 SRLNRILEIDPEDGTATVQAGVTLEDLEKALAPHGLFLPVDPSSSGTATIGGNIATNAGG 141
Query: 192 MKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSS-GPDFNHVILGSE 239
++ YG D ++ + +V G + R R R + G D + +GSE
Sbjct: 142 LRSLRYGLTRDNVLGLRVVLPDGEILRLGRKLRKDNAGYDLTALFVGSE 190
>gnl|CDD|129482 TIGR00387, glcD, glycolate oxidase, subunit GlcD. This protein,
the glycolate oxidase GlcD subunit, is similar in
sequence to that of several D-lactate dehydrogenases,
including that of E. coli. The glycolate oxidase has
been found to have some D-lactate dehydrogenase activity
[Energy metabolism, Other].
Length = 413
Score = 60.2 bits (146), Expect = 1e-10
Identities = 32/108 (29%), Positives = 54/108 (50%), Gaps = 1/108 (0%)
Query: 133 RVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGM 192
+N IL +D NL A ++ G+ +LE+ + +P S S++GG +A A GM
Sbjct: 50 HMNKILEIDVVNLTAVVQPGVRNLELEQAVEEHNLFYPPDPSSQISSTIGGNIAENAGGM 109
Query: 193 KKNLYGNIEDLLVQVTMVTARGT-LERPCRGPRVSSGPDFNHVILGSE 239
+ YG D ++ + +VTA G L + + +G D + +GSE
Sbjct: 110 RGLKYGTTVDYVLGLEVVTADGEILRIGGKTAKDVAGYDLTGLFVGSE 157
>gnl|CDD|178402 PLN02805, PLN02805, D-lactate dehydrogenase [cytochrome].
Length = 555
Score = 38.8 bits (90), Expect = 0.002
Identities = 41/168 (24%), Positives = 72/168 (42%), Gaps = 27/168 (16%)
Query: 90 IPDVVVWPVYITFGKYSEHSDTQISEKFD-------PAGNQTQISN----------VPIR 132
IPDVVV+P SE ++I + + P G T I + +
Sbjct: 133 IPDVVVFP-------RSEEEVSKIVKSCNKYKVPIVPYGGATSIEGHTLAPHGGVCIDMS 185
Query: 133 RVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGM 192
+ S+ L +++ +E GI +L L G +P +++GG ATR SG
Sbjct: 186 LMKSVKALHVEDMDVVVEPGIGWLELNEYLEPYGLFFPLDPGPG--ATIGGMCATRCSGS 243
Query: 193 KKNLYGNIEDLLVQVTMVTARG-TLERPCRGPRVSSGPDFNHVILGSE 239
YG + D ++ + +V G ++ R + ++G D +++GSE
Sbjct: 244 LAVRYGTMRDNVISLKVVLPNGDVVKTASRARKSAAGYDLTRLVIGSE 291
>gnl|CDD|200381 TIGR04130, FnlA, UDP-N-acetylglucosamine
4,6-dehydratase/5-epimerase. The FnlA enzyme is the
first step in the biosynthesis of UDP-FucNAc from
UDP-GlcNAc in E. coli (along with FnlB and FnlC). The
proteins identified by this model include FnlA homologs
in the O-antigen clusters of O4, O25, O26, O29 (Shigella
D11), O118, O145 and O172 serotype strains, all of which
produce O-antigens containing FucNAc (or the further
modified FucNAm). A homolog from Pseudomonas aerugiosa
serotype O11, WbjB, also involved in the biosynthesis of
UDP-FucNAc has been characterized and is now believed to
carry out both the initial 4,6-dehydratase reaction and
the subsequent epimerization of the resulting methyl
group at C-5. A phylogenetic tree of related sequences
shows a distinct clade of enzymes involved in the
biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This
clade appears to be descendant from the common ancestor
of the Pseudomonas and E. coli fucose-biosynthesis
enzymes. It has been hypothesized that the first step in
the biosynthesis of these two compounds may be the same,
and thus that these enzymes all have the same function.
At present, lacking sufficient confirmation of this, the
current model trusted cutoff only covers the tree
segment surrounding the E. coli genes. The clades
containing the Pseudomonas and QuiNAc biosynthesis
enzymes score above the noise cutoff. Immediately below
the noise cutoff are enzymes involved in the
biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again
may or may not produce the same product.
Length = 337
Score = 30.3 bits (68), Expect = 0.77
Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 13/67 (19%)
Query: 72 HGQTLYEVFSLRQTGLKRI---------PDVVVWPVYITFGKYSEHSDTQISEKFDPAGN 122
HG+ LYE R+ + I PD+ + +GKY EH D +ISE D +
Sbjct: 256 HGEKLYEALLSREEMIAAIDMGDYYRVPPDLR----DLNYGKYVEHGDRRISEVEDYNSH 311
Query: 123 QTQISNV 129
TQ +V
Sbjct: 312 NTQRLDV 318
>gnl|CDD|224490 COG1574, COG1574, Predicted metal-dependent hydrolase with the
TIM-barrel fold [General function prediction only].
Length = 535
Score = 30.4 bits (69), Expect = 0.89
Identities = 12/37 (32%), Positives = 14/37 (37%), Gaps = 7/37 (18%)
Query: 140 LDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSY 176
E+ A A RELNS G T H+ Y
Sbjct: 204 PAEELEAAAARAA-------RELNSLGITGVHDMAGY 233
>gnl|CDD|238625 cd01300, YtcJ_like, YtcJ_like metal dependent amidohydrolases. YtcJ
is a Bacillus subtilis ORF of unknown function. The
Arabidopsis homolog LAF3 has been identified as a factor
required for photochrome A signalling.
Length = 479
Score = 30.4 bits (69), Expect = 0.94
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 6/62 (9%)
Query: 133 RVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGM 192
+ ++ + A + A REL S G T+ H+ + + A+G
Sbjct: 169 VLEAVPPPTPEERRAALRAAA------RELASLGVTTVHDAGGGAADDIEAYRRLAAAGE 222
Query: 193 KK 194
Sbjct: 223 LT 224
>gnl|CDD|236989 PRK11809, putA, trifunctional transcriptional regulator/proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1318
Score = 29.2 bits (66), Expect = 2.1
Identities = 18/49 (36%), Positives = 19/49 (38%), Gaps = 15/49 (30%)
Query: 173 PDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCR 221
P YEF L GM + LY QV A G L RPCR
Sbjct: 505 PGQYEFQCL--------HGMGEPLYE-------QVVGKVADGKLNRPCR 538
>gnl|CDD|233525 TIGR01678, FAD_lactone_ox, sugar 1,4-lactone oxidases. This model
represents a family of at least two different sugar 1,4
lactone oxidases, both involved in synthesizing ascorbic
acid or a derivative. These include L-gulonolactone
oxidase (EC 1.1.3.8) from rat and
D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from
Saccharomyces cerevisiae. Members are proposed to have
the cofactor FAD covalently bound at a site specified by
Prosite motif PS00862; OX2_COVAL_FAD; 1.
Length = 438
Score = 28.3 bits (63), Expect = 4.5
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 133 RVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVA--TRAS 190
++N +L D++ +EAGI L +L+ GY S S S+ G ++ T S
Sbjct: 65 KMNKVLQFDKEKKQITVEAGIRLYQLHEQLDEHGY-SMSNLGSISEVSVAGIISTGTHGS 123
Query: 191 GMKKNLYGNIEDLLVQVTMVTARGTL 216
+K +G + +V +T++TA G +
Sbjct: 124 SIK---HGILATQVVALTIMTADGEV 146
>gnl|CDD|183043 PRK11230, PRK11230, glycolate oxidase subunit GlcD; Provisional.
Length = 499
Score = 27.4 bits (61), Expect = 7.1
Identities = 30/109 (27%), Positives = 46/109 (42%), Gaps = 4/109 (3%)
Query: 133 RVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGM 192
R N IL ++ A ++ G+ + + G +P S S+GG VA A G+
Sbjct: 108 RFNRILDINPVGRRARVQPGVRNLAISQAAAPHGLYYAPDPSSQIACSIGGNVAENAGGV 167
Query: 193 KKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVIL--GSE 239
YG L++V ++T G E G P F+ + L GSE
Sbjct: 168 HCLKYGLTVHNLLKVEILTLDG--EALTLGSDALDSPGFDLLALFTGSE 214
>gnl|CDD|226220 COG3696, COG3696, Putative silver efflux pump [Inorganic ion
transport and metabolism].
Length = 1027
Score = 27.3 bits (61), Expect = 9.2
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 37 KLICLGIKLGSEVLSLLEATNVSVS-----TQGEDRLIRAHGQ 74
KL G+ L +V + L+A N + GE+ LIRA G
Sbjct: 195 KLAAYGVSLE-DVTNALKANNANAGGGFIERGGEEYLIRAVGY 236
>gnl|CDD|178364 PLN02764, PLN02764, glycosyltransferase family protein.
Length = 453
Score = 27.3 bits (60), Expect = 9.3
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 157 DLERELNSR--GYTSGHEPDSYEFSSLGGWV 185
D REL R + SG+EPDS F +LG V
Sbjct: 238 DKTRELEERWVKWLSGYEPDSVVFCALGSQV 268
>gnl|CDD|237153 PRK12642, flgF, flagellar basal body rod protein FlgF; Reviewed.
Length = 241
Score = 26.9 bits (60), Expect = 9.9
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 8/45 (17%)
Query: 42 GIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTG 86
+K V+S + V+ +QG+ L G L +TG
Sbjct: 38 EVKF-DTVVSDTASKKVAFVSQGKSYLSTEAG-------PLTKTG 74
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
0.316 0.134 0.397
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,966,392
Number of extensions: 1096997
Number of successful extensions: 698
Number of sequences better than 10.0: 1
Number of HSP's gapped: 696
Number of HSP's successfully gapped: 15
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
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 (21.6 bits)
S2: 58 (26.0 bits)