RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14926
(140 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 103 bits (258), Expect = 1e-26
Identities = 35/78 (44%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 4 ADFFLIYL-QVIA-RRQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDVFFAKNP 61
D L L ++A RR DLKLI+ SAT+DA++FS +FGN P I GRT+PV++ +
Sbjct: 178 TDILLGLLKDLLARRRDDLKLIIMSATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEA 237
Query: 62 VEDY-VDSAVKQALQIHL 78
DY + A+ A+ IHL
Sbjct: 238 EADYILLDAIVAAVDIHL 255
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 69.7 bits (171), Expect = 8e-15
Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 3/72 (4%)
Query: 5 DFFLIYL-QVIARRQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDVFFAKNPVE 63
DF L YL +++ RR DLK+I+TSAT+D ++FS F N P + GRT+PV+V + P+
Sbjct: 203 DFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRY--RPIV 260
Query: 64 DYVDSAVKQALQ 75
+ D + LQ
Sbjct: 261 EEADDTERDQLQ 272
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 69.0 bits (169), Expect = 1e-14
Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 3/72 (4%)
Query: 5 DFFLIYL-QVIARRQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDVFFAKNPVE 63
DF L YL Q++ RR DLK+I+TSAT+D ++FS F N P + GRT+PV+V + P+
Sbjct: 196 DFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRY--RPLV 253
Query: 64 DYVDSAVKQALQ 75
+ + L+
Sbjct: 254 EEQEDDDLDQLE 265
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 49.8 bits (119), Expect = 6e-08
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 17 RQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDV----FFAKNPVEDYVDSAVKQ 72
R+DLK++ SAT+D ++ S+ + P GR+FPV++ +ED V AV+
Sbjct: 144 REDLKILAMSATLDGERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEH 203
Query: 73 ALQIH 77
AL
Sbjct: 204 ALASE 208
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 43.4 bits (103), Expect = 1e-05
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 17 RQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDVFF----AKNPVEDYVDSAVKQ 72
R DLKL++ SAT+D D+ + P GR+FPV+ + A ++ V A +
Sbjct: 147 RDDLKLLIMSATLDNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAE 206
Query: 73 ALQ 75
L+
Sbjct: 207 LLR 209
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 29.6 bits (67), Expect = 0.48
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 22 LIVTSATM--DADKFSNFFGNVPTFHIPGRT-FPVDVFFAKN 60
L + +AT+ D D+ FF N HIPG T FP+ + KN
Sbjct: 324 LFLMTATLEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKN 365
>gnl|CDD|233704 TIGR02064, dsrA, sulfite reductase, dissimilatory-type alpha
subunit. Dissimilatory sulfite reductase catalyzes the
six-electron reduction of sulfite to sulfide, as the
terminal reaction in dissimilatory sulfate reduction. It
remains unclear however, whether trithionate and
thiosulfate serve as intermediate compounds to sulfide,
or as end products of sulfite reduction. Sulfite
reductase is a multisubunit enzyme composed of dimers of
either alpha/beta or alpha/beta/gamma subunits, each
containing a siroheme and iron sulfur cluster prosthetic
center. Found in sulfate-reducing bacteria, these genes
are commonly located in an unidirectional gene cluster.
This model describes the alpha subunit of sulfite
reductase [Central intermediary metabolism, Sulfur
metabolism].
Length = 402
Score = 29.4 bits (66), Expect = 0.54
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 100 SGPKLRYLGLCIEKAQKELALFTTLPLATG-RSNFADSLH 138
SG LR C+ A+ E A + TL + D LH
Sbjct: 150 SGSNLRTPESCVGPARCEFACYDTLKACYELTMEYQDELH 189
>gnl|CDD|238424 cd00828, elong_cond_enzymes, "elongating" condensing enzymes are
a subclass of decarboxylating condensing enzymes,
including beta-ketoacyl [ACP] synthase, type I and II
and polyketide synthases.They are characterized by the
utlization of acyl carrier protein (ACP) thioesters as
primer substrates, as well as the nature of their
active site residues.
Length = 407
Score = 29.3 bits (66), Expect = 0.65
Identities = 9/38 (23%), Positives = 13/38 (34%), Gaps = 2/38 (5%)
Query: 37 FFGNVPTFHIPGRTFPVDVFFAKNPVEDYVDSAVKQAL 74
G +PT IPG + A ++AL
Sbjct: 49 VAGQIPTGDIPGWD--AKRTGIVDRTTLLALVATEEAL 84
>gnl|CDD|217492 pfam03321, GH3, GH3 auxin-responsive promoter.
Length = 513
Score = 28.0 bits (63), Expect = 1.6
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 33 KFSNFFGNVPTFHIPGRTFPV-DVFFAKNPVEDYVDSAVKQAL 74
+ + F+ P F GRT V +F K E+ ++ AVK AL
Sbjct: 365 RVTGFYNYTPQFEFVGRTKHVLSLFGEKLTEEE-LEKAVKNAL 406
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 28.3 bits (62), Expect = 1.7
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 14 IARRQDLKLIVTSATMDADK 33
+A+R+DL + +TS+ MDADK
Sbjct: 1865 LAKRRDLSIELTSSDMDADK 1884
>gnl|CDD|226097 COG3567, COG3567, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 452
Score = 26.8 bits (59), Expect = 4.5
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 8 LIYLQVIARRQDLKLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVD 54
L L V+ R ++ + S MD D FS FG + I T V+
Sbjct: 140 LKSLTVLDR---WRVALGSGQMDQDVFSETFGQPRCYQITAGTSSVE 183
>gnl|CDD|130618 TIGR01555, phge_rel_HI1409, phage-related protein, HI1409 family.
This model describes an uncharacterized family of
proteins found in prophage regions of a number of
bacterial genomes, including Haemophilus influenzae,
Xylella fastidiosa, Salmonella typhi, and Enterococcus
faecalis. Distantly related proteins can be found in the
prophage-bearing plasmids of Borrelia burgdorferi
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 404
Score = 26.8 bits (59), Expect = 5.0
Identities = 9/35 (25%), Positives = 19/35 (54%)
Query: 21 KLIVTSATMDADKFSNFFGNVPTFHIPGRTFPVDV 55
+++ +D D FS +G + ++ I GR+ +V
Sbjct: 132 SGKISNGQIDEDVFSPNYGQIESYEINGRSLLNNV 166
>gnl|CDD|173849 cd01160, LCAD, Long chain acyl-CoA dehydrogenase. LCAD is an
acyl-CoA dehydrogenases (ACAD), which is found in the
mitochondria of eukaryotes and in some prokaryotes. It
catalyzes the alpha, beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of LCAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. LCAD acts as a homodimer.
Length = 372
Score = 26.7 bits (59), Expect = 5.3
Identities = 9/41 (21%), Positives = 15/41 (36%)
Query: 37 FFGNVPTFHIPGRTFPVDVFFAKNPVEDYVDSAVKQALQIH 77
F N H GR + AK + + + +Q+H
Sbjct: 292 FLDNCAWRHEQGRLDVAEASMAKYWATELQNRVAYECVQLH 332
>gnl|CDD|129965 TIGR00887, 2A0109, phosphate:H+ symporter. This model represents
the phosphate uptake symporter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Anions].
Length = 502
Score = 26.6 bits (59), Expect = 5.3
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 34 FSNFFGNVPTFHIPGRTFP 52
F+NF N TF +PG FP
Sbjct: 404 FANFGPNATTFIVPGEVFP 422
>gnl|CDD|227199 COG4862, MecA, Negative regulator of genetic competence,
sporulation and motility [Posttranslational
modification, protein turnover, chaperones / Signal
transduction mechanisms / Cell motility and secretion].
Length = 224
Score = 25.8 bits (57), Expect = 8.6
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 9 IYLQVIARRQDLKLIVTSATMDADKFSNF 37
+++QV A Q L++IVT + ++ + +
Sbjct: 60 LWIQVQALPQGLEVIVTKSKIEGEGPDDL 88
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 26.0 bits (58), Expect = 9.1
Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 17/96 (17%)
Query: 56 FFAKNPVEDYVDSAVKQALQIHLIPNPDQKYPWPCFQKVRFGRY----------SGPKLR 105
FF ++PVE ++ A +I L P+ ++ +++ G G +R
Sbjct: 414 FFVRDPVELEIEGAEPLEAKIPLHPDRPERG----EREIPVGGKVYVSSDDLEAEGKMVR 469
Query: 106 YLGLC---IEKAQKELALFTTLPLATGRSNFADSLH 138
+ L I + A + + L R N A +
Sbjct: 470 LMDLFNVEITGVSVDKARYHSDDLEEARKNKAPIIQ 505
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 0.142 0.439
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,273,880
Number of extensions: 640535
Number of successful extensions: 670
Number of sequences better than 10.0: 1
Number of HSP's gapped: 669
Number of HSP's successfully gapped: 20
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.6 bits)