RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1909
(92 letters)
>gnl|CDD|130539 TIGR01474, ubiA_proteo, 4-hydroxybenzoate polyprenyl transferase,
proteobacterial. This model represents a family of
integral membrane proteins that condenses
para-hydroxybenzoate with any of several
polyprenyldiphosphates. Heterologous expression studies
suggest that for, many but not all members, the activity
seen (e.g. octaprenyltransferase in E. coli) reflects
available host isoprenyl pools rather than enzyme
specificity. A fairly deep split by both clustering
(UPGMA) and phylogenetics (NJ tree) separates this group
(mostly Proteobacterial and mitochondrial), with several
characterized members, from another group (mostly
archaeal and Gram-positive bacterial) lacking
characterized members [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 281
Score = 72.7 bits (179), Expect = 5e-17
Identities = 28/69 (40%), Positives = 42/69 (60%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHL 74
D+++DI +G+KSTA+ FGD TK +L G +M+ L G+++G Y+L L+ L
Sbjct: 184 DKEDDIKIGVKSTALRFGDNTKPWLGGLYALMILLLALAGLIAGLGPVYYLGLAAAALLL 243
Query: 75 ASQIYHLDI 83
QI LDI
Sbjct: 244 IRQIATLDI 252
>gnl|CDD|178405 PLN02809, PLN02809, 4-hydroxybenzoate nonaprenyltransferase.
Length = 289
Score = 72.4 bits (178), Expect = 6e-17
Identities = 30/70 (42%), Positives = 46/70 (65%)
Query: 14 RDRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSH 73
+D+++D+ +G+KSTA+ FGD TKL+L+GFG + L G +G WPY+ L+ H
Sbjct: 189 QDKEDDLKVGVKSTALRFGDDTKLWLTGFGAASIGGLALSGYNAGLGWPYYAGLAAAAGH 248
Query: 74 LASQIYHLDI 83
LA QI +D+
Sbjct: 249 LAWQIQTVDL 258
>gnl|CDD|237229 PRK12848, ubiA, 4-hydroxybenzoate octaprenyltransferase; Reviewed.
Length = 282
Score = 55.2 bits (134), Expect = 1e-10
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHL 74
DR +D+ +G+KSTAILFG KL + ++ L G L G W Y+ L + +
Sbjct: 186 DRDDDLKIGIKSTAILFGRYDKLIIGLLQLATLALLAWAGWLLGLGWAYYWGLLVAAALF 245
Query: 75 ASQIYHL 81
Q L
Sbjct: 246 VYQ-QKL 251
>gnl|CDD|183808 PRK12878, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
Length = 314
Score = 54.6 bits (132), Expect = 2e-10
Identities = 28/69 (40%), Positives = 39/69 (56%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHL 74
D+++D +G+KSTA LFGD TK +L F G+ + + L+G L L +HL
Sbjct: 216 DKEDDALIGVKSTARLFGDHTKTWLVLFYGLAVLLMGLAFWLAGVPLLALLGLLAAAAHL 275
Query: 75 ASQIYHLDI 83
A QI LDI
Sbjct: 276 AWQIARLDI 284
>gnl|CDD|237240 PRK12870, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
Length = 290
Score = 50.0 bits (120), Expect = 1e-08
Identities = 18/67 (26%), Positives = 33/67 (49%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHL 74
DR++D+ +G+ S+AI FG + F + + L G+L P+++ L++
Sbjct: 190 DREDDLRIGVNSSAIFFGRYAPEAIGLFFALTVGFLAILGVLLELHLPFWIGLAIAAVLW 249
Query: 75 ASQIYHL 81
A Q L
Sbjct: 250 ARQYRRL 256
>gnl|CDD|237228 PRK12847, ubiA, 4-hydroxybenzoate polyprenyltransferase; Reviewed.
Length = 285
Score = 47.2 bits (113), Expect = 9e-08
Identities = 21/69 (30%), Positives = 37/69 (53%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHL 74
D+K+D+ +G+KSTAI FG+KT+ Y+ + + + GI+S ++L++
Sbjct: 189 DKKDDLKIGVKSTAIYFGNKTRKYILRLYIISLILWLILGIISSLHNIFYLAILAAAGIF 248
Query: 75 ASQIYHLDI 83
Q LD
Sbjct: 249 YYQYKLLDF 257
>gnl|CDD|223459 COG0382, UbiA, 4-hydroxybenzoate polyprenyltransferase and related
prenyltransferases [Coenzyme metabolism].
Length = 289
Score = 45.0 bits (107), Expect = 7e-07
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWP-YFLSLSLIGSH 73
D + D GLKS +LFG K L L+ + + LV G+L+G Y L L +
Sbjct: 191 DIEGDRKAGLKSLPVLFGIKKALALALLLLLASALLVLLGLLAGLLGLIYLLGLLVAALL 250
Query: 74 LASQIYHLDI 83
L QI +D+
Sbjct: 251 LLYQILIVDV 260
>gnl|CDD|171787 PRK12873, ubiA, prenyltransferase; Reviewed.
Length = 294
Score = 34.3 bits (79), Expect = 0.004
Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 21/95 (22%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQT---WPYFL------ 65
DR++D +GL S+A+ G + + L ++ WP++L
Sbjct: 194 DRRDDAKIGLNSSALSLGSNALKTVQICYFLTSIFLALAAFIAQVGFIFWPFWLIASIGM 253
Query: 66 ------------SLSLIGSHLASQIYHLDIVFLGL 88
S+ IG+H ++Q+ ++ LGL
Sbjct: 254 QRDILKLFPEKQSIKTIGNHFSNQVILGSLLLLGL 288
>gnl|CDD|224491 COG1575, MenA, 1,4-dihydroxy-2-naphthoate octaprenyltransferase
[Coenzyme metabolism].
Length = 303
Score = 29.1 bits (66), Expect = 0.22
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 14 RDRKEDISLGLKSTAILFGDK--TKLY--LSGFGGVMMSSLVTCGILSGQTWPYFLSLSL 69
RD +EDI G + A+ G K KLY L + + V G+ + L+L L
Sbjct: 199 RDIEEDIRNGKYTLAVRLGRKNARKLYAALLVVAYLAIVIFVILGLFPVWGLLFLLALPL 258
Query: 70 IGSH 73
Sbjct: 259 AIRA 262
>gnl|CDD|236475 PRK09352, PRK09352, 3-oxoacyl-(acyl carrier protein) synthase III;
Reviewed.
Length = 319
Score = 28.9 bits (66), Expect = 0.29
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 23/63 (36%)
Query: 2 QHKDVL----DKQSR---PRDRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCG 54
+K+VL +K SR DR ST +LFGD G G V++ + G
Sbjct: 131 AYKNVLVIGAEKLSRIVDWTDR---------STCVLFGD-------GAGAVVLGASEEPG 174
Query: 55 ILS 57
ILS
Sbjct: 175 ILS 177
>gnl|CDD|216260 pfam01040, UbiA, UbiA prenyltransferase family.
Length = 259
Score = 28.6 bits (64), Expect = 0.39
Identities = 14/69 (20%), Positives = 24/69 (34%)
Query: 14 RDRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSH 73
RD + D G+++ + G K L L L+ +L L++ L+
Sbjct: 169 RDVEGDRKAGIRTLPVRLGRKRALALYALLLAAALLLLLLLLLLLAPLLLLLAVLLLALA 228
Query: 74 LASQIYHLD 82
L L
Sbjct: 229 LLVAARLLR 237
>gnl|CDD|220359 pfam09719, C_GCAxxG_C_C, Putative redox-active protein
(C_GCAxxG_C_C). This entry represents a putative
redox-active protein of about 140 residues, with four
perfectly conserved Cys residues. It includes a CGAXXG
motif. Most members are found within one or two loci of
transporter or oxidoreductase genes. A member from
Geobacter sulfurreducens, located in a molybdenum
transporter operon, has a TAT (twin-arginine
translocation) signal sequence for Sec-independent
transport across the plasma membrane, a hallmark of
bound prosthetic groups such as FeS clusters.
Length = 119
Score = 26.0 bits (58), Expect = 2.1
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 40 SGFGGVMMSSLVTCGILSG 58
SGFGG M + TCG L+G
Sbjct: 27 SGFGGGMGGAGGTCGALTG 45
>gnl|CDD|216920 pfam02182, YDG_SRA, YDG/SRA domain. The function of this domain
is unknown, it contains a conserved motif YDG after
which it has been named.
Length = 154
Score = 26.1 bits (58), Expect = 2.2
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 54 GILSGQTWPYFLSLSLIGSHLASQ 77
G+ G + Y + L ++G H Q
Sbjct: 8 GVEVGDIFFYRVELCVVGLHRPHQ 31
>gnl|CDD|237013 PRK11898, PRK11898, prephenate dehydratase; Provisional.
Length = 283
Score = 26.3 bits (59), Expect = 2.3
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 70 IGSHLASQIYHLDIV 84
I S LA+++Y L+I+
Sbjct: 150 IASELAAELYGLEIL 164
>gnl|CDD|133461 cd06851, GT_GPT_like, This family includes eukaryotic
UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT) and
archaeal GPT-like glycosyltransferases. Eukaryotic GPT
catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to
dolichol-P to form GlcNAc-P-P-dolichol. The reaction is
the first step in the assembly of dolichol-linked
oligosaccharide intermediates and is essential for
eukaryotic N-linked glycosylation. GPT activity has been
identified in all eukaryotic cells examined to date.
Evidence for the existence of the N-glycosylation
pathway in archaea has emerged and genes responsible for
the pathway have been identified. A glycosyl transferase
gene Mv1751 in M. voltae encodes for the enzyme that
carries out the first step in the pathway, the
attachment of GlcNAc to a dolichol lipid carrier in the
membrane. A lethal mutation in the alg7 (GPT) gene in
Saccharomyces cerevisiae was successfully complemented
with Mv1751, the archaeal gene, indicating eukaryotic
and archaeal enzymes may use the same substrates and are
evolutionarily closer than the bacterial enzyme, which
uses a different substrate.
Length = 223
Score = 25.9 bits (57), Expect = 3.1
Identities = 8/41 (19%), Positives = 16/41 (39%)
Query: 40 SGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHLASQIYH 80
+GF ++ +L ++ L L + LA Y+
Sbjct: 137 AGFTTIISFALAISLLVQQNYEIGIACLCLAFASLAFLYYN 177
>gnl|CDD|233337 TIGR01273, speA, arginine decarboxylase, biosynthetic. Two
alternative pathways can convert arginine to putrescine.
One is decarboxylation by this enzyme followed by
removal of the urea moeity by agmatinase. In the other,
the ureohydrolase (arginase) acts first, followed by
ornithine decarboxylase. This pathway leads to
spermidine biosynthesis, hence the gene symbol speA. A
distinct biodegradative form is also pyridoxal
phosphate-dependent but is not similar in sequence
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 624
Score = 25.8 bits (57), Expect = 4.1
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 66 SLSLIGSHLASQIYHLDIVFLGL----QFYC 92
SL L+ H+ SQI ++D + G+ +FYC
Sbjct: 238 SLQLLHFHIGSQISNIDDIKKGVREAARFYC 268
>gnl|CDD|182086 PRK09802, PRK09802, DNA-binding transcriptional regulator AgaR;
Provisional.
Length = 269
Score = 25.6 bits (56), Expect = 4.5
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 8/41 (19%)
Query: 50 LVTCGILSGQTWPYFLSLSLIGSH--LASQIYHLDIVFLGL 88
L+T G L Q S S G + Q YH D++FLG+
Sbjct: 153 LMTGGHLRRQ------SQSFYGDQAEQSLQNYHFDMLFLGV 187
>gnl|CDD|238426 cd00830, KAS_III, Ketoacyl-acyl carrier protein synthase III
(KASIII) initiates the elongation in type II fatty acid
synthase systems. It is found in bacteria and plants.
Elongation of fatty acids in the type II systems occurs
by Claisen condensation of malonyl-acyl carrier protein
(ACP) with acyl-ACP. KASIII initiates this process by
specifically using acetyl-CoA over acyl-CoA.
Length = 320
Score = 25.6 bits (57), Expect = 4.6
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 16/44 (36%)
Query: 5 DVLDKQSRPRDRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMS 48
+ L + DR STA+LFGD G G V++
Sbjct: 139 ETLSRILDWTDR---------STAVLFGD-------GAGAVVLE 166
>gnl|CDD|237014 PRK11899, PRK11899, prephenate dehydratase; Provisional.
Length = 279
Score = 25.2 bits (56), Expect = 5.9
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 66 SLSLIGSHLASQIYHLDIV 84
S++ + S LA+++Y LDI+
Sbjct: 144 SMAALASRLAAELYGLDIL 162
>gnl|CDD|132306 TIGR03262, PhnU2, putative 2-aminoethylphosphonate ABC transporter,
permease protein. [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 546
Score = 25.0 bits (55), Expect = 7.7
Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 16/71 (22%)
Query: 3 HKDVLDKQSRP----RDRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSG 58
+ L +S P +R D + + I L+ G + +SLV
Sbjct: 260 QRAQLSSRSVPYQPKPNRVRDAACLVYCAIISA-----ALLAVVGMAVYASLVK------ 308
Query: 59 QTWPYFLSLSL 69
WPY LSL+L
Sbjct: 309 -FWPYNLSLTL 318
>gnl|CDD|223537 COG0461, PyrE, Orotate phosphoribosyltransferase [Nucleotide
transport and metabolism].
Length = 201
Score = 24.5 bits (54), Expect = 7.9
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 21/66 (31%)
Query: 15 DRKEDISLGLKSTAILFGDKTKLYLSGFGGVMMSSLVTCGILSGQTWPYFLSLSLIGSH- 73
++E L L+ A+ FG+ T LS SG+ PY++ L L +
Sbjct: 2 YKRELAELLLEKGALKFGEFT---LS----------------SGRKSPYYVDLRLFLTGP 42
Query: 74 -LASQI 78
L I
Sbjct: 43 ELLQLI 48
>gnl|CDD|233105 TIGR00728, OPT_sfam, oligopeptide transporter, OPT superfamily.
This superfamily has two main branches. One branch
contains a tetrapeptide transporter demonstrated
experimentally in three different species of yeast. The
other family contains EspB of Myxococcus xanthus, a
protein required for normal rather than delayed
sporulation after cellular aggregation; its role is
unknown but is compatible with transport of a signalling
molecule. Homology between the two branches of the
superfamily is seen most easily at the ends of the
protein. The central regions are poorly conserved within
each branch and may not be homologous between branches.
Length = 606
Score = 24.7 bits (54), Expect = 8.9
Identities = 9/49 (18%), Positives = 14/49 (28%)
Query: 42 FGGVMMSSLVTCGILSGQTWPYFLSLSLIGSHLASQIYHLDIVFLGLQF 90
F G + + S + IGS L + + LG
Sbjct: 209 FPGFTAFQTFGGLGSGSIGFGWQQSSAYIGSGLITPFTVGLNILLGFVL 257
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 0.141 0.427
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,506,472
Number of extensions: 358414
Number of successful extensions: 437
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 38
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
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: 53 (24.1 bits)