RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5540
(135 letters)
>gnl|CDD|221410 pfam12077, DUF3556, Transmembrane protein of unknown function
(DUF3556). This family of transmembrane proteins is
functionally uncharacterized. This protein is found in
bacteria. Proteins in this family are typically between
576 to 592 amino acids in length.
Length = 574
Score = 30.8 bits (70), Expect = 0.19
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 35 NVFLIVGTTTLFFIFDCPFLATRVSPWIPVV--GVITFLFVLGALF--RTSF 82
NVF I G LF LA SPW+ V V+ + +LG LF + SF
Sbjct: 340 NVFFIFGVLFLFVGHAGVGLADLSSPWLLAVLIAVLAGVPILGNLFPDKVSF 391
>gnl|CDD|240088 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain.
LOX is a member of the family of FMN-containing
alpha-hydroxyacid oxidases and catalyzes the oxidation
of l-lactate using molecular oxygen to generate pyruvate
and H2O2. This family occurs in both prokaryotes and
eukaryotes. Members of this family include
flavocytochrome b2 (FCB2), glycolate oxidase (GOX),
lactate monooxygenase (LMO), mandelate dehydrogenase
(MDH), and long chain hydroxyacid oxidase (LCHAO).
Length = 351
Score = 28.2 bits (63), Expect = 1.2
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 79 RTSFSDPGVIPRATSDEAAFIETQIELKNVNLDSPTFRPP 118
+F+ ++PR + +T EL + L +P P
Sbjct: 41 TRAFNHKQIVPRVLQGVES-PDTSTELLGIKLKTPIIMAP 79
>gnl|CDD|234419 TIGR03965, mycofact_glyco, mycofactocin system glycosyltransferase.
Members of this protein family are putative
glycosyltransferases, members of pfam00535 (glycosyl
transferase family 2). Members appear mostly in the
Actinobacteria, where they appear to be part of a system
for converting a precursor peptide (TIGR03969) into a
novel redox carrier designated mycofactocin. A radical
SAM enzyme, TIGR03962, is a proposed to be a key
maturase for mycofactocin.
Length = 467
Score = 28.2 bits (63), Expect = 1.3
Identities = 10/54 (18%), Positives = 17/54 (31%)
Query: 38 LIVGTTTLFFIFDCPFLATRVSPWIPVVGVITFLFVLGALFRTSFSDPGVIPRA 91
++V TL C A R + + + L R + + RA
Sbjct: 314 MVVPAWTLLAWLGCLAAAGRSARLALLSALPALADAATRLRRARRAGAPLPTRA 367
>gnl|CDD|225930 COG3395, COG3395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 413
Score = 27.7 bits (62), Expect = 1.9
Identities = 18/69 (26%), Positives = 25/69 (36%), Gaps = 4/69 (5%)
Query: 52 PFLATRVSPWIPVVGVITF---LFVLGALF-RTSFSDPGVIPRATSDEAAFIETQIELKN 107
F V P +P+ G F LFV G L + + V P S + Q + K
Sbjct: 105 GFSIAVVVPALPLNGRTVFGGYLFVNGVLVDESGMARDPVTPMKDSYLPRHVAKQTKGKI 164
Query: 108 VNLDSPTFR 116
+D R
Sbjct: 165 GLVDLADVR 173
>gnl|CDD|216274 pfam01062, Bestrophin, Bestrophin, RFP-TM, chloride channel.
Bestrophin is a 68-kDa basolateral plasma membrane
protein expressed in retinal pigment epithelial cells
(RPE). It is encoded by the VMD2 gene, which is mutated
in Best macular dystrophy, a disease characterized by a
depressed light peak in the electrooculogram. VMD2
encodes a 585-amino acid protein with an approximate
mass of 68 kDa which has been designated bestrophin.
Bestrophin shares homology with the Caenorhabditis
elegans RFP gene family, named for the presence of a
conserved arginine (R), phenylalanine (F), proline (P),
amino acid sequence motif. Bestrophin is a plasma
membrane protein, localised to the basolateral surface
of RPE cells consistent with a role for bestrophin in
the generation or regulation of the EOG light peak.
Bestrophin and other RFP family members represent a new
class of chloride channels, indicating a direct role for
bestrophin in generating the light peak. The VMD2 gene
underlying Best disease was shown to represent the first
human member of the RFP-TM protein family. More than 97%
of the disease-causing mutations are located in the
N-terminal RFP-TM domain implying important functional
properties. The bestrophins are four-pass transmembrane
chloride-channel proteins, and the RFP-TM or bestrophin
domain extends from the N-terminus through approximately
350 amino acids and contains all of the TM domains as
well as nearly all reported disease causing mutations.
Interestingly, the RFP motif is not conserved
evolutionarily back beyond Metazoa, neither is it in
plant members.
Length = 284
Score = 27.5 bits (62), Expect = 2.3
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 42 TTTLFFIFDCPF-LATRVSPWIPVVGVITFLFVLG 75
L+ + PF L + + P+ V+ F F G
Sbjct: 217 AVYLYCLL-LPFGLQDTLGWFTPLFTVLIFYFFFG 250
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as well
as three of the four conserved transmembrane regions
found in this family of palmitoyltransferase enzymes.
Length = 167
Score = 26.3 bits (58), Expect = 4.8
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 76 ALFRTSFSDPGVIPRATSDEAAFIETQIEL-KNVNLDSPTFRP------PPRTK 122
+ F+T F+DPG +P+ +++ + E + D F PPR+
Sbjct: 3 SYFKTIFTDPGYVPKNPTEKEQEKQPDEESEEGDEEDELKFCSTCNIIKPPRSH 56
>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA;
Provisional.
Length = 919
Score = 26.7 bits (60), Expect = 4.8
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 5/26 (19%)
Query: 88 IPRATSDEAAFIET--QIELKNVNLD 111
I +ATSD ET Q+E++NV LD
Sbjct: 258 IDQATSD---LRETLEQMEIQNVELD 280
>gnl|CDD|182737 PRK10794, PRK10794, cell wall shape-determining protein;
Provisional.
Length = 370
Score = 26.2 bits (58), Expect = 6.4
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 15/47 (31%)
Query: 21 GRVMMGPSAAVFYVNVFLIVGTTTLFFIFDCPFLATRVSPWIPVVGV 67
GRVM G + +V VF+ +G VS +PVVGV
Sbjct: 303 GRVMAGGLMLILFVYVFVNIGM---------------VSGILPVVGV 334
>gnl|CDD|131331 TIGR02278, PaaN-DH, phenylacetic acid degradation protein paaN.
This enzyme is proposed to act in the ring-opening step
of phenylacetic acid degradation which follows ligation
of the acid with coenzyme A (by PaaF) and hydroxylation
by a multicomponent non-heme iron hydroxylase complex
(PaaGHIJK). Gene symbols have been standardized in. This
enzyme is related to aldehyde dehydrogenases and has
domains which are members of the pfam00171 and pfam01575
families. This family includes paaN genes from
Pseudomonas, Sinorhizobium, Rhodopseudomonas,
Escherichia, Deinococcus and Corynebacterium. Another
homology family (TIGR02288) includes several other
species.
Length = 663
Score = 26.3 bits (58), Expect = 7.1
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 55 ATRVSPWIPVVGVITFLFVLGALFRTSFSDPGVIPR----ATSDEAAFIETQI 103
ATR W+ + G I LF +L R D +IP S + +F I
Sbjct: 88 ATRRDNWVDIDGGIGTLFTYSSLGRRELPDANLIPEDEFEPLSKDGSFQGRHI 140
>gnl|CDD|217785 pfam03901, Glyco_transf_22, Alg9-like mannosyltransferase family.
Members of this family are mannosyltransferase enzymes.
At least some members are localised in endoplasmic
reticulum and involved in GPI anchor biosynthesis.
Length = 412
Score = 25.8 bits (57), Expect = 8.3
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 32 FYVNVFLIVGTTTLFFIFDCPFLATRVSPWIPVVGVITFLFVLGAL 77
F + I+G L FI L +R+ + + ++ +LFV
Sbjct: 264 FSNGLPNILGPFLLAFILGPLVLVSRL--LLLLAPILIWLFVYSLQ 307
>gnl|CDD|237166 PRK12666, PRK12666, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 528
Score = 26.0 bits (58), Expect = 8.6
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 26 GPSAAVFY----VNVFLIVGTTTLFFIFDCPFLATRVSPWIPVVGVITFLF-VLGAL 77
P AA+F V ++ I+ +TL F + A W+ G+ T F +G L
Sbjct: 242 APVAALFAIMTKVGIYAILRLSTLLFGPEAGASAGFGQDWLLPGGLATLAFGAIGVL 298
>gnl|CDD|132249 TIGR03205, pimA, dicarboxylate--CoA ligase PimA. PimA, a member of
a large family of acyl-CoA ligases, is found in a
characteristic operon pimFABCDE for the metabolism of
pimelate and related compounds. It is found, so far, in
Bradyrhizobium japonicum and several strains of
Rhodopseudomonas palustris. PimA from R. palustris was
shown to be active as a CoA ligase for C(7) to C(14)
dicarboxylates and fatty acids.
Length = 541
Score = 26.1 bits (57), Expect = 8.6
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 103 IELKNVNLDSPT-FRPPPRTKEIVIRGQTVKLKY 135
IEL V+LD PT PP E+ IRG V Y
Sbjct: 374 IELDVVSLDDPTKVLPPGEVGELRIRGPNVTRGY 407
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
0.328 0.142 0.450
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,065,443
Number of extensions: 647345
Number of successful extensions: 961
Number of sequences better than 10.0: 1
Number of HSP's gapped: 959
Number of HSP's successfully gapped: 59
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (24.1 bits)