RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780534|ref|YP_003064947.1| acyl carrier protein
[Candidatus Liberibacter asiaticus str. psy62]
(85 letters)
>gnl|CDD|177047 CHL00124, acpP, acyl carrier protein; Validated.
Length = 82
Score = 67.7 bits (166), Expect = 6e-13
Identities = 38/73 (52%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 6 DDVFEAVKEVILSQLTSVKEDQIVESARFIEELGADSLDVVELVMIFEEKFSLEIPEESA 65
+D+FE V+ ++ QL +++ ++ A F +LGADSLDVVELVM EEKF +EIP+E A
Sbjct: 4 NDIFEKVQSIVAEQL-GIEKSEVTLDANFTRDLGADSLDVVELVMAIEEKFDIEIPDEDA 62
Query: 66 NKILTVKDAVDFI 78
KI T+++AVDFI
Sbjct: 63 EKISTLQEAVDFI 75
>gnl|CDD|36959 KOG1748, KOG1748, KOG1748, Acyl carrier protein/NADH-ubiquinone
oxidoreductase, NDUFAB1/SDAP subunit [Energy production
and conversion, Lipid transport and metabolism,
Secondary metabolites biosynthesis, transport and
catabolism].
Length = 131
Score = 62.6 bits (152), Expect = 2e-11
Identities = 31/82 (37%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 4 ANDDVFEAVKEVILSQLTSVKEDQIVESARFIEELGADSLDVVELVMIFEEKFSLEIPEE 63
A +V + V +V+ + ++ + F ++LG DSLD VE+VM EE+F +EIP+E
Sbjct: 50 AKKEVVDRVLDVVKKFD-KIDPSKLTTDSDFFKDLGLDSLDTVEIVMALEEEFGIEIPDE 108
Query: 64 SANKILTVKDAVDFIRKAKQTN 85
A+KI TV+DA D+I
Sbjct: 109 DADKIKTVRDAADYIADKPDVK 130
>gnl|CDD|30585 COG0236, AcpP, Acyl carrier protein [Lipid metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 80
Score = 46.8 bits (111), Expect = 1e-06
Identities = 37/77 (48%), Positives = 50/77 (64%), Gaps = 1/77 (1%)
Query: 7 DVFEAVKEVILSQLTSVKEDQIVESARFIEELGADSLDVVELVMIFEEKFSLEIPEESAN 66
+ E VK++I QL V E++I A F+E+LG DSLD+VELVM EE+F +EIP+E
Sbjct: 5 AIEERVKDIIAEQL-GVDEEEITTEASFVEDLGLDSLDLVELVMALEEEFGIEIPDEELE 63
Query: 67 KILTVKDAVDFIRKAKQ 83
I TV D VD+I +
Sbjct: 64 NIKTVGDLVDYIEELLA 80
>gnl|CDD|144221 pfam00550, PP-binding, Phosphopantetheine attachment site. A
4'-phosphopantetheine prosthetic group is attached
through a serine. This prosthetic group acts as a a
'swinging arm' for the attachment of activated fatty
acid and amino-acid groups. This domain forms a four
helix bundle. This family includes members not included
in Prosite. The inclusion of these members is supported
by sequence analysis and functional evidence. The
related domain of Listonella anguillarum angR has the
attachment serine replaced by an alanine.
Length = 67
Score = 37.9 bits (89), Expect = 6e-04
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 16 ILSQLTSVKEDQIVESARFIEELGADSLDVVELVMIFEEKFSLEIPEESANKILTVKDAV 75
I++++ + D+I +LG DSL VEL+ EE+F +EIP + T+ +
Sbjct: 6 IVAEVLGIPPDEIDPDDDL-FDLGLDSLLAVELLARLEEEFGVEIPPSDLFEHPTLGELA 64
Query: 76 DFI 78
++
Sbjct: 65 AYL 67
>gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive..
Length = 325
Score = 27.1 bits (60), Expect = 1.3
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 10 EAVKEVILSQLTSVKEDQIVESARFIEELGADSLDVVELVMIFEEKFSLEIPEESANKIL 69
AV +++ L V V+ AR IEE GAD+L++ + + S E+ IL
Sbjct: 96 RAVSIPVIASLNGVSAGGWVDYARQIEEAGADALELNIYALPTDPDISGAEVEQRYLDIL 155
Query: 70 T-VKDAV 75
VK AV
Sbjct: 156 RAVKSAV 162
>gnl|CDD|73380 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs..
Length = 336
Score = 26.6 bits (59), Expect = 1.6
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 13/52 (25%)
Query: 7 DVFEAVKEVILSQLT-----SVKE--------DQIVESARFIEELGADSLDV 45
+V +AV+ V S + + VE A+ ++ELG D +DV
Sbjct: 209 EVVDAVRAVWPEDKPLFVRISATDWVEGGWDLEDSVELAKALKELGVDLIDV 260
>gnl|CDD|73368 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue
on tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in
some archaea. Most dihydrouridines are found in the D
loop of t-RNAs. The role of dihydrouridine in tRNA is
currently unknown, but may increase conformational
flexibility of the tRNA. It is likely that different
family members have different substrate specificities,
which may overlap. 1VHN, a putative flavin
oxidoreductase, has high sequence similarity to DUS.
The enzymatic mechanism of 1VHN is not known at the
present..
Length = 231
Score = 25.5 bits (56), Expect = 3.4
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 19 QLTSVKEDQIVESARFIEELGADSLDV 45
QL + + E+A+ +EELGAD +D+
Sbjct: 60 QLGGSDPETLAEAAKIVEELGADGIDL 86
>gnl|CDD|73402 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively..
Length = 296
Score = 25.1 bits (55), Expect = 4.2
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 2 PNANDDVFEAVKEV----ILSQLTSVKEDQIVESARFIEELGADSLDVVELVM 50
P A ++ +AVK+ ++ +LT D IVE AR EE GAD L ++ +
Sbjct: 139 PEAVAEIVKAVKKATDVPVIVKLTPNVTD-IVEIARAAEEAGADGLTLINTLK 190
>gnl|CDD|113131 pfam04348, LppC, LppC putative lipoprotein. This family includes
several bacterial outer membrane antigens, whose
molecular function is unknown.
Length = 535
Score = 24.8 bits (54), Expect = 6.0
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 4 ANDDVFEAVKEVI-LSQLTSVKEDQ 27
A D EA K I + QL S K Q
Sbjct: 110 ARGDAIEAAKARIQMDQLLSGKRKQ 134
>gnl|CDD|176233 cd08272, MDR6, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 326
Score = 24.1 bits (53), Expect = 10.0
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 30 ESARFIEELGADSLD-----VVELVM 50
E A F LGAD + VVE V
Sbjct: 179 EKAAFARSLGADPIIYYRETVVEYVA 204
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.313 0.131 0.330
Gapped
Lambda K H
0.267 0.0826 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 883,202
Number of extensions: 37833
Number of successful extensions: 130
Number of sequences better than 10.0: 1
Number of HSP's gapped: 130
Number of HSP's successfully gapped: 24
Length of query: 85
Length of database: 6,263,737
Length adjustment: 54
Effective length of query: 31
Effective length of database: 5,096,851
Effective search space: 158002381
Effective search space used: 158002381
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.2 bits)