RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9810
(154 letters)
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 109 bits (275), Expect = 6e-29
Identities = 47/65 (72%), Positives = 50/65 (76%)
Query: 2 WQIPLGRRFRSLKLWFVLRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMGL 61
WQIPLGRRFRSLKLW VLRL GV+ LQ YIR I LAKEFEQLV D RFEV+ + L
Sbjct: 353 WQIPLGRRFRSLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQLVAQDSRFEVVTPRIFSL 412
Query: 62 VCFRL 66
VCFRL
Sbjct: 413 VCFRL 417
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 105 bits (265), Expect = 5e-28
Identities = 44/67 (65%), Positives = 49/67 (73%)
Query: 1 HWQIPLGRRFRSLKLWFVLRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMG 60
WQIPL RRFR LKLWFVLR GV+ LQ IR+ + LAK FE LVR D RFE+ E +G
Sbjct: 307 DWQIPLSRRFRILKLWFVLRSYGVEGLQNQIRRHVELAKYFEALVRKDSRFEICAERGLG 366
Query: 61 LVCFRLK 67
LVCFRLK
Sbjct: 367 LVCFRLK 373
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 81.3 bits (200), Expect = 1e-18
Identities = 37/65 (56%), Positives = 43/65 (66%)
Query: 2 WQIPLGRRFRSLKLWFVLRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMGL 61
WQI L RRFRSLKLW VLRL G + L+ +IR ++LAK FE V D FEV+ L
Sbjct: 401 WQISLSRRFRSLKLWMVLRLYGSENLRNFIRDHVNLAKHFEDYVAQDPSFEVVTTRYFSL 460
Query: 62 VCFRL 66
VCFRL
Sbjct: 461 VCFRL 465
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 72.2 bits (178), Expect = 1e-15
Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 10 FRSLKLWFVLRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMGLVCFRLK 67
R+LKLW LR G E+I + + LAK +L+R+D FE++ E + LVCFRLK
Sbjct: 229 VRALKLWATLRRFGRDGYGEHIDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLK 286
>gnl|CDD|215948 pfam00494, SQS_PSY, Squalene/phytoene synthase.
Length = 262
Score = 60.0 bits (146), Expect = 1e-11
Identities = 28/81 (34%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 73 LRKFDYENFLCTLLLPKALQNASFVIRAFNIEVAKVQDNVSDVTTGQARLTFWDNAIDKL 132
LRK +L +LLLP L+ A + AF E + D VSD G+ARL +W +A+D
Sbjct: 1 LRKHSRSFYLASLLLPPELRRAVAALYAFCREADDIVDEVSDPLIGRARLDWWRDALDAA 60
Query: 133 ---YTDQVPAHPVVQELNKVI 150
HPV++ L +
Sbjct: 61 FAGRRLGPSTHPVLRALADTV 81
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 48.5 bits (116), Expect = 2e-07
Identities = 16/61 (26%), Positives = 33/61 (54%)
Query: 10 FRSLKLWFVLRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMGLVCFRLKTA 69
++L L+ LR LG + ++ + + + LA+ + + FE++ E + +V FRLK
Sbjct: 323 RQALALYANLRRLGREGYRKLLDRTLELARYLAEELEKLGDFELVNEPELPIVAFRLKDD 382
Query: 70 K 70
+
Sbjct: 383 E 383
>gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD. The genes of this family
are often found in the same genetic locus with
squalene-hopene cyclase genes, and are never associated
with genes for the metabolism of phytoene. In the
organisms Zymomonas mobilis and Bradyrhizobium japonicum
these genes have been characterized as squalene
synthases (farnesyl-pyrophosphate ligases). Often, these
genes appear in tandem with the HpnC gene which appears
to have resulted from an ancient gene duplication event.
Presumably these proteins form a heteromeric complex,
but this has not yet been experimentally demonstrated.
Length = 266
Score = 44.6 bits (106), Expect = 5e-06
Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 85 LLLPKALQNASFVIRAFNIEVAKVQDNVSDVTTGQARLTFWDNAIDKLYTDQVPAHPVVQ 144
LLP + A + AF EV + D SD QA+L +W ID+LY P+HPV +
Sbjct: 13 RLLPPERRRAMTALYAFCREVDDIVDEDSDPEVAQAKLAWWRAEIDRLY-AGAPSHPVAR 71
Query: 145 EL 146
L
Sbjct: 72 AL 73
>gnl|CDD|224478 COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism].
Length = 288
Score = 35.8 bits (83), Expect = 0.004
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 81 FLCTLLLPKALQNASFVIRAFNIEVAKVQDNVSDVTTGQARLTFWDNAIDKLYTDQ-VPA 139
+L LLLP + A + + AF E V D VSD L W +D ++ Q
Sbjct: 25 YLAILLLPPEKREAVWALYAFCREADDVVDGVSDPDLPAEILLAWRRELDGDFSGQPASD 84
Query: 140 HPVVQELNKVIS 151
HPV+ L +V
Sbjct: 85 HPVLAALVEVAR 96
>gnl|CDD|173831 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Synthases,
head-to-head. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze a head-to-head (HH)
(1'-1) condensation reaction. This CD includes squalene
and phytoene synthases which catalyze the 1'-1
condensation of two 15-carbon (farnesyl) and 20-carbon
(geranylgeranyl) isoprenyl diphosphates, respectively.
The catalytic site consists of a large central cavity
formed by mostly antiparallel alpha helices with two
aspartate-rich regions (DXXXD) located on opposite
walls. These residues mediate binding of prenyl
phosphates. A two-step reaction has been proposed for
squalene synthase (farnesyl-diphosphate
farnesyltransferase) in which, two molecules of FPP
react to form a stable cyclopropylcarbinyl diphosphate
intermediate, and then the intermediate undergoes
heterolysis, isomerization, and reduction with NADPH to
form squalene, a precursor of cholestrol. The carotenoid
biosynthesis enzyme, phytoene synthase (CrtB), catalyzes
the condensation reaction of two molecules of
geranylgeranyl diphosphate to produce phytoene, a
precursor of beta-carotene. These enzymes produce the
triterpene and tetraterpene precursors for many diverse
sterol and carotenoid end products and are widely
distributed among eukareya, bacteria, and archaea.
Length = 265
Score = 31.4 bits (72), Expect = 0.14
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 81 FLCTLLLPKALQNASFVIRAFNIEVAKVQDNVSD-VTTGQARLTFWDNAIDKLYTDQVPA 139
+L + LLP L+ A + AF + D+ + A L + +D Y P
Sbjct: 15 YLASRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYWGGAPT 74
Query: 140 HPVVQELNKV 149
HPV++ L +
Sbjct: 75 HPVLRALADL 84
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed.
Length = 637
Score = 31.6 bits (72), Expect = 0.16
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 101 FNIEVAKVQDNVSDVTTGQARLTFWDNAIDKLY 133
+ A+VQD TG+ R++FW L
Sbjct: 311 RDDRTAEVQDIELADGTGRVRVSFWGEKAKILE 343
>gnl|CDD|239920 cd04474, RPA1_DBD_A, RPA1_DBD_A: A subfamily of OB folds
corresponding to the second OB fold, the ssDNA-binding
domain (DBD)-A, of human RPA1 (also called RPA70). RPA1
is the large subunit of Replication protein A (RPA). RPA
is a nuclear ssDNA-binding protein (SSB) which appears
to be involved in all aspects of DNA metabolism
including replication, recombination, and repair. RPA
also mediates specific interactions of various nuclear
proteins. In animals, plants, and fungi, RPA is a
heterotrimer with subunits of 70KDa (RPA1), 32kDa
(RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1
contains three other OB folds: DBD-B, DBD-C, and RPA1N.
The major DNA binding activity of human RPA (hRPA) and
Saccharomyces cerevisiae RPA (ScRPA) is associated with
DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in
trimerization. The ssDNA-binding mechanism is believed
to be multistep and to involve conformational change.
Although ScRPA and the hRPA have similar ssDNA-binding
properties, they differ functionally. Antibodies to hRPA
do not cross-react with ScRPA, and null mutations in the
ScRPA subunits are not complemented by corresponding
human genes. Also, ScRPA cannot support Simian virus 40
(SV40) DNA replication in vitro, whereas human RPA can.
Length = 104
Score = 28.4 bits (64), Expect = 0.67
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 8/42 (19%)
Query: 111 NVSDVTTGQARLTFWDNAIDKLYTDQVPAHPVVQELNKVISI 152
++ D G+ R TF+++A+DK Y D + E+ KV I
Sbjct: 40 DLLDEDGGEIRATFFNDAVDKFY-DLL-------EVGKVYYI 73
>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed.
Length = 485
Score = 28.6 bits (64), Expect = 1.4
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 12/43 (27%)
Query: 99 RAFNIEVAKVQDNVSDVTTGQARLTFWDN----AIDKLYTDQV 137
R N+EVA TG R+ FWD A ++L QV
Sbjct: 91 RVINVEVAD--------ETGSVRVAFWDEQAVAAEEELEVGQV 125
>gnl|CDD|239978 cd04605, CBS_pair_MET2_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the MET2 domain. Met2 is a key enzyme in
the biosynthesis of methionine. It encodes a homoserine
transacetylase involved in converting homoserine to
O-acetyl homoserine. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 110
Score = 26.9 bits (60), Expect = 2.6
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 97 VIRAFNIEVAKVQDN--VSDVTTGQARLTFWDNAID----KLYTDQVPAHPVVQELNKVI 150
++ +++I A +D V D+ T D ID K+ + A PVV N+VI
Sbjct: 40 IVTSWDISKAVARDKKSVEDIMTRNVITATPDEPIDVAARKMERHNISALPVVDAENRVI 99
Query: 151 SIV 153
I+
Sbjct: 100 GII 102
>gnl|CDD|169427 PRK08402, PRK08402, replication factor A; Reviewed.
Length = 355
Score = 26.7 bits (59), Expect = 5.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 117 TGQARLTFWDNAIDKLYTD 135
TG+AR+ WD + K Y
Sbjct: 109 TGRARVVLWDAKVAKYYNK 127
>gnl|CDD|173162 PRK14699, PRK14699, replication factor A; Provisional.
Length = 484
Score = 26.9 bits (59), Expect = 5.5
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 117 TGQARLTFWDNAIDKLYTDQVPAHPVVQ 144
TG+ +LT WDN D + ++ A +Q
Sbjct: 104 TGKIKLTLWDNMADLIKAGKIKAGQTLQ 131
>gnl|CDD|163511 TIGR03799, NOD_PanD_pyr, putative pyridoxal-dependent aspartate
1-decarboxylase. This enzyme is proposed here to be a
form of aspartate 1-decarboxylase, pyridoxal-dependent,
that represents a non-orthologous displacement to the
more widely distributed pyruvoyl-dependent form
(TIGR00223). Aspartate 1-decarboxylase makes
beta-alanine, used usually in pathothenate biosynthesis,
by decarboxylation from asparatate. A number of species
with the PanB and PanC enzymes, however, lack PanD. This
protein family occurs in a number of Proteobacteria that
lack PanD. This enzyme family appears to be a
pyridoxal-dependent enzyme (see pfam00282). The family
was identified by Partial Phylogenetic Profiling;
members in Geobacter sulfurreducens, G. metallireducens,
and Pseudoalteromonas atlantica are clustered with the
genes for PanB and PanC. We suggest the gene symbol panP
(panthothenate biosynthesis enzyme, Pyridoxal-dependent)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 522
Score = 27.0 bits (60), Expect = 5.6
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 19 LRLLGVKYLQEYIRKQISLAKEFEQLVRSDDRFEVIYEVLMGLVCFRLKTAKV 71
L ++G K + I + I AK F L++ FE++ E + L+ +R +V
Sbjct: 390 LHIIGRKGYELLIDQSIEKAKYFADLIQQQPDFELVTEPELCLLTYRYVPEEV 442
>gnl|CDD|235747 PRK06222, PRK06222, ferredoxin-NADP(+) reductase subunit alpha;
Reviewed.
Length = 281
Score = 26.3 bits (59), Expect = 7.2
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 4/23 (17%)
Query: 136 QVPAHPVVQEL----NKVISIVG 154
P +P+ + L NKVI+I+G
Sbjct: 110 IAPVYPIAKALKEAGNKVITIIG 132
>gnl|CDD|205430 pfam13250, DUF4041, Domain of unknown function (DUF4041). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, archaea and viruses,
and is approximately 60 amino acids in length. The
family is found in association with pfam10544.
Length = 56
Score = 24.4 bits (54), Expect = 7.9
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 96 FVIRAFNIEV----AKVQDNVSDVTTGQARLTFWDNAIDKLYT 134
++RAFN E AKV +++ T + R+ I+KL
Sbjct: 2 LMLRAFNGECDAAIAKV--KYNNIDTMEKRIEKSFEQINKLGE 42
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
0.327 0.141 0.422
Gapped
Lambda K H
0.267 0.0821 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,945,045
Number of extensions: 721823
Number of successful extensions: 805
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 34
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (24.8 bits)