RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1354
(118 letters)
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 195
Score = 102 bits (257), Expect = 1e-28
Identities = 37/87 (42%), Positives = 57/87 (65%), Gaps = 6/87 (6%)
Query: 7 IPTDHIGVIATYRNQVSLLKRLLDK------DIEINTVDQYQGRDKSIILYSSTCTSKSK 60
IG+I YR QV L+K+LL + DIE+NTVD +QGR+K +I++S+ +++
Sbjct: 107 EKNKDIGIITPYRAQVRLIKKLLKRKFGGEPDIEVNTVDGFQGREKDVIIFSTVRSNEKG 166
Query: 61 ESKILNDRKRLTVAISRAKHKLIILGD 87
L+D +RL VA++RAK LII+G+
Sbjct: 167 GIGFLSDPRRLNVALTRAKRGLIIVGN 193
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 81.4 bits (201), Expect = 2e-19
Identities = 38/89 (42%), Positives = 61/89 (68%), Gaps = 3/89 (3%)
Query: 6 GIPTDHIGVIATYRNQVSLLKRLLDK---DIEINTVDQYQGRDKSIILYSSTCTSKSKES 62
G+P + IGVI Y QV LL++LL+ DIE+++VD +QGR+K +I+ S +++ E
Sbjct: 524 GVPANDIGVITPYDAQVDLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEV 583
Query: 63 KILNDRKRLTVAISRAKHKLIILGDLQVI 91
L D +RL VA++RA+ KLI++GD + +
Sbjct: 584 GFLKDLRRLNVALTRARRKLIVIGDSRTL 612
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 72.3 bits (177), Expect = 4e-16
Identities = 40/93 (43%), Positives = 58/93 (62%), Gaps = 4/93 (4%)
Query: 3 LISGIPTDHIGVIATYRNQVSLLKRLLD---KDIEINTVDQYQGRDKSIILYSST-CTSK 58
L G+ + IGVI+ YR QVSL++RLL+ K +E+ TVD +QGR+K +I+ S
Sbjct: 639 LKDGLEENDIGVISPYRAQVSLIRRLLNEAGKGVEVGTVDGFQGREKDVIILSLVRSNDD 698
Query: 59 SKESKILNDRKRLTVAISRAKHKLIILGDLQVI 91
E L D +RL VA++RAK KLI++G +
Sbjct: 699 KGEIGFLGDPRRLNVALTRAKRKLIVVGSSSTL 731
>gnl|CDD|222209 pfam13538, UvrD_C_2, Family description. This domain is found at
the C-terminus of a wide variety of helicase enzymes.
This domain has a AAA-like structural fold.
Length = 105
Score = 28.5 bits (64), Expect = 0.38
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 67 DRKRLTVAISRAKHKLIIL 85
R+ L A++RAK KL ++
Sbjct: 87 FRRLLYTAVTRAKKKLYLV 105
>gnl|CDD|227786 COG5499, COG5499, Predicted transcription regulator containing HTH
domain [Transcription].
Length = 120
Score = 28.6 bits (64), Expect = 0.40
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 57 SKSKESKILNDRKRLTVAISRAKHK 81
SKS+ S IL+ R+ LT+ + H+
Sbjct: 85 SKSRVSNILSGRRALTLEHIKKLHQ 109
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 28.2 bits (63), Expect = 1.0
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 60 KESKILNDRKRLTVAISRAKHKLIILGDLQVI 91
S +L R+ L AI+RA+ +LI+ GD +
Sbjct: 644 SHSPML-SRELLYTAITRARDRLILYGDEKAF 674
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 28.1 bits (63), Expect = 1.1
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 33 IEINTVDQYQGR-DKSIILYSSTCTSKSKESKILNDRKRLTVAISRAKHKLIILG 86
+ TV + QG S+ L T ++D + L VA++R + L IL
Sbjct: 176 VRATTVHEVQGLTFDSVTLVLDKDTDLL----SISDPELLYVALTRHRKSLHILT 226
>gnl|CDD|216227 pfam00982, Glyco_transf_20, Glycosyltransferase family 20. Members
of this family belong to glycosyl transferase family 20.
OtsA (Trehalose-6-phosphate synthase) is homologous to
regions in the subunits of yeast trehalose-6-phosphate
synthase/phosphate complex.
Length = 470
Score = 28.0 bits (63), Expect = 1.1
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 14/75 (18%)
Query: 19 RNQVSLLKRLLDKDIEINTVDQYQGRDKSIILY---------SSTCTSKSKESKILNDRK 69
R+ +S RLL + + +Y GR S+ + S S S + K+ ++
Sbjct: 207 RHFLSCCSRLLGLETTSDGGVEYGGRTVSVGAFPIGIDPGRIESGLKSPSVQEKVKELKE 266
Query: 70 RLTVAISRAKHKLII 84
R K KLI+
Sbjct: 267 RF-----GNKKKLIL 276
>gnl|CDD|192770 pfam11520, Cren7, Chromatin protein Cren7. Cren7 is a chromatin
protein found in Crenarchaeota and has a higher affinity
for double-stranded DNA than for single-stranded DNA.
The protein contains negative DNA supercoils and is
associated with genomic DNA in vivo.Cren7 interacts with
duplex DNA through a beta-sheet and a long flexible
loop. The function has not been completely determined
but it is thought that the protein may have a role
similar to that of archaeal proteins in Euryarchaea.
Length = 59
Score = 26.3 bits (58), Expect = 1.3
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 90 VIIAIVNCPNTGRY 103
V I + P TG+Y
Sbjct: 36 VKIGLFKDPETGKY 49
>gnl|CDD|215042 PLN00054, PLN00054, photosystem I reaction center subunit N;
Provisional.
Length = 139
Score = 26.7 bits (59), Expect = 2.3
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 2/21 (9%)
Query: 58 KSKESKILNDRKRLTVAISRA 78
KSK +K LND+KRL A S A
Sbjct: 62 KSKANKELNDKKRL--ATSGA 80
>gnl|CDD|224074 COG1152, CdhA, CO dehydrogenase/acetyl-CoA synthase alpha subunit
[Energy production and conversion].
Length = 772
Score = 27.1 bits (60), Expect = 2.4
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 47 SIILYSSTCTSKSKESKILNDRKRLTVAISRAKHKLIILGDLQVIIAIVNCPN 99
++I ++ K ++ K+ R + R I++G + IIA++ CPN
Sbjct: 458 NMIEKAAQKRIKEEKGKVRAGRGPIPDVEIRNVGVPIVMGTIPGIIAVIGCPN 510
>gnl|CDD|238897 cd01916, ACS_1, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
decarbonylase, is found in acetogenic and methanogenic
organisms and is responsible for the synthesis and
breakdown of acetyl-CoA. ACS forms a heterotetramer
with carbon monoxide dehydrogenase (CODH) consisting of
two ACS and two CODH subunits. CODH reduces carbon
dioxide to carbon monoxide and ACS then synthesizes
acetyl-CoA from carbon monoxide, CoA, and a methyl group
donated by another protein (CoFeSP). ACS has three
structural domains, an N-terminal rossman fold domain
with a helical region at its N-terminus which interacts
with CODH, and two alpha + beta fold domains. A Ni-Fe-S
center referred to as the A-cluster is located in the
C-terminal domain. A large cavity exists between the
three domains which may bind CoA.
Length = 731
Score = 26.6 bits (59), Expect = 3.3
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 83 IILGDLQVIIAIVNCPN 99
I+LGD+ +IA+V C N
Sbjct: 459 IVLGDIPGVIALVGCSN 475
>gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex
subunit alpha; Validated.
Length = 781
Score = 26.5 bits (59), Expect = 3.7
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 83 IILGDLQVIIAIVNCPN 99
I+LGD+ +IA V C N
Sbjct: 498 IVLGDIPGVIAFVGCSN 514
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 26.7 bits (59), Expect = 4.0
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 61 ESKILNDRKRLTVAISRAKHKLIILGDLQVIIAIVNCPN 99
S +L R+ L I+RAK +L + D + + A + N
Sbjct: 545 NSPVLT-RELLYTGITRAKDQLSVWSDKETLNAAIKRKN 582
>gnl|CDD|215446 PLN02832, PLN02832, glutamine amidotransferase subunit of
pyridoxal 5'-phosphate synthase complex.
Length = 248
Score = 26.2 bits (58), Expect = 5.0
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 12 IGVIA---TYRNQVSLLKRLLDKDIEINTVDQYQGRDKSII 49
IGV+A ++ ++ L+RL + +E+ +Q +G II
Sbjct: 4 IGVLALQGSFNEHIAALRRLGVEAVEVRKPEQLEGVSGLII 44
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 26.2 bits (58), Expect = 5.4
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 71 LTVAISRAKHKLIILGD 87
L VA++RAK KLI++G
Sbjct: 861 LYVALTRAKEKLILVGS 877
>gnl|CDD|222277 pfam13637, Ank_4, Ankyrin repeats (many copies).
Length = 54
Score = 24.5 bits (54), Expect = 5.8
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 18 YRNQVSLLKRLLDKDIEINTVD 39
++ L+K LL+K ++IN D
Sbjct: 10 ISGRLELVKYLLEKGVDINRTD 31
>gnl|CDD|131958 TIGR02912, sulfite_red_C, sulfite reductase, subunit C. Members of
this protein family include the C subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum.
Note that any one of these enzymes may have secondary
substates such as NH2OH, SeO3(2-), and SO3(2-).
Heterologous expression of the anaerobic sulfite
reductase of Salmonella confers on Escherichia coli the
ability to produce hydrogen sulfide gas from sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 314
Score = 26.0 bits (57), Expect = 6.3
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 72 TVAISRAKHKLIILGDLQVIIAIVNCPN 99
T ++ K + D V IA+ CPN
Sbjct: 119 TTKFAKRIEKAVFPNDYHVKIALTGCPN 146
>gnl|CDD|226482 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
function prediction only].
Length = 747
Score = 26.0 bits (57), Expect = 6.8
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 66 NDRKRLTVAISRAKHKLIILG 86
D + L VA++RA H L I G
Sbjct: 724 QDLRDLYVAVTRALHSLYIFG 744
>gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional.
Length = 684
Score = 25.7 bits (57), Expect = 6.8
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 68 RKRLTVAISRAKHKLIILGD 87
R+ L VA++RAKH++ +L +
Sbjct: 643 RRLLYVALTRAKHRVWLLFN 662
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 25.9 bits (57), Expect = 7.3
Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 37 TVDQYQGRDKSIILYSSTCTSKSKESKILNDRKRLTVAISRAKHKLIILGDLQVI-IAIV 95
++ + QG + ++ + R L A++RAK ++I++G + IA
Sbjct: 652 SIHKSQGSEFPTVI-----LPIHTAHMRMLYRNLLYTALTRAKKRVILVGSAEAFDIAAA 706
Query: 96 N 96
Sbjct: 707 R 707
>gnl|CDD|237796 PRK14712, PRK14712, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1623
Score = 25.6 bits (55), Expect = 7.8
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 67 DRKRLTVAISRAKHKLIILGDLQVIIAIVNCPNTGRYGNLGQIPGTDGN 115
DR+ L I A+ K LG +QV++ ++N N R G L ++ + N
Sbjct: 1103 DRRVLNSMIHDAREKAGELGQVQVMVPVLNTANI-RDGELRRLSTWENN 1150
>gnl|CDD|130147 TIGR01075, uvrD, DNA helicase II. Designed to identify uvrD
members of the uvrD/rep subfamily [DNA metabolism, DNA
replication, recombination, and repair].
Length = 715
Score = 25.5 bits (56), Expect = 9.3
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 65 LNDRKRLT-VAISRAKHKLII 84
L + +RL V I+RA KL I
Sbjct: 587 LEEERRLAYVGITRAMQKLTI 607
>gnl|CDD|166510 PLN02869, PLN02869, fatty aldehyde decarbonylase.
Length = 620
Score = 25.2 bits (55), Expect = 9.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 27 RLLDKDIEINTVDQYQGRDKSIIL 50
R++DK IE VD+ + D I+
Sbjct: 78 RIVDKGIEFEQVDRERNWDDQILF 101
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 25.2 bits (55), Expect = 10.0
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 73 VAISRAKHKLIILGDLQVIIAIVNCPNTGRYGNLGQ 108
++ISRA K+ Q++ A+ CP G YG
Sbjct: 324 ISISRASAKIFYPARFQLVAAMNPCP-CGHYGGKNT 358
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
0.318 0.136 0.379
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: 5,815,037
Number of extensions: 489627
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 468
Number of HSP's successfully gapped: 41
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)