RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3902
(181 letters)
>gnl|CDD|221912 pfam13086, AAA_11, 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 = 220
Score = 77.8 bits (192), Expect = 5e-18
Identities = 25/47 (53%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 6 FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSK 52
F +IDEA QATEPE L+P+ L + VVL GD QL PTV S
Sbjct: 177 FDVVIIDEAAQATEPETLIPLLLGCK---KVVLVGDHKQLPPTVLSP 220
Score = 77.8 bits (192), Expect = 5e-18
Identities = 25/47 (53%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 66 FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSK 112
F +IDEA QATEPE L+P+ L + VVL GD QL PTV S
Sbjct: 177 FDVVIIDEAAQATEPETLIPLLLGCK---KVVLVGDHKQLPPTVLSP 220
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 77.7 bits (191), Expect = 5e-17
Identities = 42/119 (35%), Positives = 52/119 (43%), Gaps = 20/119 (16%)
Query: 62 PSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
F + +IDEA QATEP L+ +S V+L GD QL PTVF K L
Sbjct: 485 KKYEFDYVIIDEASQATEPSALIALSRA----KKVILVGDHKQLPPTVFFKESSPEGLSA 540
Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
SL ERL P +V L YR P+I+ SS +FY+ L H
Sbjct: 541 SLFERLIDNG----------------PEVVYLLRVQYRMHPDIIAFSSKVFYNGRLEVH 583
Score = 58.4 bits (141), Expect = 2e-10
Identities = 25/57 (43%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 6 FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTP 62
F + +IDEA QATEP L+ +S V+L GD QL PTVF K LS
Sbjct: 489 FDYVIIDEASQATEPSALIALSRA----KKVILVGDHKQLPPTVFFKESSPEGLSAS 541
>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 = 65.6 bits (160), Expect = 5e-13
Identities = 40/116 (34%), Positives = 53/116 (45%), Gaps = 22/116 (18%)
Query: 65 YFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLL 124
F VIDEA QA EP L+P+ L R ++LAGD QL PT+ S ++LEL +L
Sbjct: 361 EFDVAVIDEASQAMEPSCLIPL-LKAR---KLILAGDHKQLPPTILSHDAEELEL--TLF 414
Query: 125 ERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
ERL + P L YR +I++ S FY+ L H
Sbjct: 415 ERLIKEY----------------PERSRTLNVQYRMNQKIMEFPSREFYNGKLTAH 454
Score = 51.0 bits (122), Expect = 6e-08
Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 4/56 (7%)
Query: 5 YFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELS 60
F VIDEA QA EP L+P+ L R ++LAGD QL PT+ S ++LEL+
Sbjct: 361 EFDVAVIDEASQAMEPSCLIPL-LKAR---KLILAGDHKQLPPTILSHDAEELELT 412
>gnl|CDD|222258 pfam13604, AAA_30, 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. There is a Walker A and
Walker B.
Length = 195
Score = 36.4 bits (85), Expect = 0.003
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 10 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 47
V+DEAG ++ + L + VVL GDP QL
Sbjct: 97 VVDEAGMVGTRQMARLLRLAEKAGAKVVLVGDPAQLQA 134
Score = 36.4 bits (85), Expect = 0.003
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 70 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 107
V+DEAG ++ + L + VVL GDP QL
Sbjct: 97 VVDEAGMVGTRQMARLLRLAEKAGAKVVLVGDPAQLQA 134
>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 = 33.7 bits (78), Expect = 0.032
Identities = 18/62 (29%), Positives = 21/62 (33%), Gaps = 16/62 (25%)
Query: 119 LRISLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLV 178
L SL ERL P V L YR P+I + S+LFY L
Sbjct: 1 LDRSLFERL---------QEAG-------PEAVVMLDTQYRMHPDISEFPSELFYGGKLK 44
Query: 179 PH 180
Sbjct: 45 DG 46
>gnl|CDD|181996 PRK09619, flgD, flagellar basal body rod modification protein;
Reviewed.
Length = 218
Score = 31.7 bits (72), Expect = 0.16
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 9/72 (12%)
Query: 35 HVVLAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQATEPEVLVPISLLHRDNG 94
V++ + LG + +L L P+ T + D GQ + I L + G
Sbjct: 97 QVMVESHEITLGEDPVAG---RLTLKHPAPTLTLHITDILGQEKK------IDLGKQPAG 147
Query: 95 HVVLAGDPLQLG 106
V DP LG
Sbjct: 148 PVNFTLDPAALG 159
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 30.9 bits (70), Expect = 0.34
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 10 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 47
VIDEAG ++ + VVL GDP QL P
Sbjct: 444 VIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQP 481
Score = 30.9 bits (70), Expect = 0.34
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 70 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 107
VIDEAG ++ + VVL GDP QL P
Sbjct: 444 VIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQP 481
>gnl|CDD|218483 pfam05183, RdRP, RNA dependent RNA polymerase. This family of
proteins are eukaryotic RNA dependent RNA polymerases.
These proteins are involved in post transcriptional gene
silencing where they are thought to amplify dsRNA
templates.
Length = 508
Score = 30.2 bits (68), Expect = 0.57
Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 14/92 (15%)
Query: 26 ISLLHRDNG----HVVLAGDPLQ-------LGPTVFSKLGQQLE---LSTPSGYFTHCVI 71
+ LL + + L P + L V L + E + P V+
Sbjct: 267 LDLLRKQADENDFTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVPKSAALFGVV 326
Query: 72 DEAGQATEPEVLVPISLLHRDNGHVVLAGDPL 103
DE G E EV V +S + + L GD L
Sbjct: 327 DETGVLKEGEVFVQVSDGNDGGQYEYLEGDVL 358
Score = 29.0 bits (65), Expect = 1.6
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 2 PAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPL 43
P V+DE G E EV V +S + + L GD L
Sbjct: 317 PKSAALFGVVDETGVLKEGEVFVQVSDGNDGGQYEYLEGDVL 358
>gnl|CDD|237524 PRK13826, PRK13826, Dtr system oriT relaxase; Provisional.
Length = 1102
Score = 28.2 bits (63), Expect = 2.9
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 10 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 47
V+DEAG ++ + + + R +VL GDP QL P
Sbjct: 473 VLDEAGMVASRQMALFVEAVTRAGAKLVLVGDPEQLQP 510
Score = 28.2 bits (63), Expect = 2.9
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 70 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGP 107
V+DEAG ++ + + + R +VL GDP QL P
Sbjct: 473 VLDEAGMVASRQMALFVEAVTRAGAKLVLVGDPEQLQP 510
>gnl|CDD|217744 pfam03813, Nrap, Nrap protein. Members of this family are
nucleolar RNA-associated proteins (Nrap) which are
highly conserved from yeast (Saccharomyces cerevisiae)
to human. In the mouse, Nrap is ubiquitously expressed
and is specifically localised in the nucleolus. Nrap is
a large nucleolar protein (of more than 1000 amino
acids). Nrap appears to be associated with ribosome
biogenesis by interacting with pre-rRNA primary
transcript.
Length = 929
Score = 27.6 bits (62), Expect = 3.9
Identities = 9/39 (23%), Positives = 12/39 (30%)
Query: 38 LAGDPLQLGPTVFSKLGQQLELSTPSGYFTHCVIDEAGQ 76
LA L GP S + G+ T D +
Sbjct: 228 LATTDLTTGPLSLSSASESESKYIFFGFDTPVFFDGSRG 266
>gnl|CDD|99708 cd00004, Sortase, Sortases are cysteine transpeptidases, found in
gram-positive bacteria, that anchor surface proteins to
peptidoglycans of the bacterial cell wall envelope. They
do so by catalyzing a transpeptidation reaction in which
the surface protein substrate is cleaved at a conserved
cell wall sorting signal and covalently linked to
peptidoglycan for display on the bacterial surface.
Sortases are grouped into different classes and
subfamilies based on sequence, membrane topology,
genomic positioning, and cleavage site preference. The
different classes are called Sortase A or SrtA
(subfamily 1), B or SrtB (subfamily 2), C or SrtC
(subfamily3), D or SrtD (subfamilies 4 and 5), and E or
SrtE. In two different sortase subfamilies, the
N-terminus either functions as both a signal peptide for
secretion and a stop-transfer signal for membrane
anchoring, or it contains a signal peptide only and the
C-terminus serves as a membrane anchor. Most
gram-positive bacteria contain more than one sortase and
it is thought that the different sortases anchor
different surface protein classes. The sortase domain is
a modified beta-barrel flanked by two (SrtA) or three
(SrtB) short alpha-helices.
Length = 128
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 92 DNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTGRFLYS 134
+NG+ V+AG TVFS L + L ++Y
Sbjct: 41 ENGNTVIAGHRGGDSGTVFSDLDNLKKGDKIYLTDGGKTYVYK 83
>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 = 27.0 bits (60), Expect = 4.8
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 3/66 (4%)
Query: 70 VIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLLERLTG 129
++DE +L+ ++ V+L GDPLQ P + S L G
Sbjct: 64 ILDEYTLLPPGYILLLAAISGAKL--VILFGDPLQ-IPYHSRAPSFLIAHFPSSLSHRVG 120
Query: 130 RFLYSR 135
R
Sbjct: 121 RRTTYL 126
>gnl|CDD|226577 COG4092, COG4092, Predicted glycosyltransferase involved in capsule
biosynthesis [Cell envelope biogenesis, outer membrane].
Length = 346
Score = 27.2 bits (60), Expect = 4.9
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 15/49 (30%)
Query: 128 TGRFLYSRDMSRFYATGGYDPR----------LVTRL---VNNYRTMPE 163
T FL +R M F TGGYD R +TRL + N + +
Sbjct: 179 TNIFLINRRM--FSLTGGYDERFRGHGSEDFEFLTRLGLYIKNLPMLTK 225
>gnl|CDD|163668 cd07425, MPP_Shelphs, Shewanella-like phosphatases,
metallophosphatase domain. This family includes
bacterial, eukaryotic, and archeal proteins orthologous
to the Shewanella cold-active protein-tyrosine
phosphatase, CAPTPase. CAPTPase is an uncharacterized
protein that belongs to the Shelph (Shewanella-like
phosphatase) family of PPP (phosphoprotein
phosphatases). The PPP family is one of two known
protein phosphatase families specific for serine and
threonine. In addition to Shelps, the PPP family also
includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6,
PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase.
The PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 208
Score = 26.8 bits (60), Expect = 6.4
Identities = 25/109 (22%), Positives = 37/109 (33%), Gaps = 34/109 (31%)
Query: 91 RDNGHVVLAGDPLQLGPTV------FSKLGQQLEL---RISLL----ER--LTGRFLY-- 133
+ H+V GD GP V KL Q+ ++ L E L G F Y
Sbjct: 31 GGSTHLVQLGDIFDRGPDVIEILWLLYKLEQEAAKAGGKVHFLLGNHELMNLCGDFRYVH 90
Query: 134 ----------SRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLF 172
+ ++ GG R R+ P I+K++ LF
Sbjct: 91 PKYFNEFGGLAMRRRELFSPGGELGRW-------LRSKPVIVKVNDTLF 132
>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA
family. This group is comprised of bacterial proteins
assigned to the RluA family of pseudouridine synthases.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. The
RluA family is comprised of proteins related to
Escherichia coli RluA.
Length = 246
Score = 26.9 bits (60), Expect = 6.6
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 15/83 (18%)
Query: 17 ATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELSTPSG-YFTHCVIDEAG 75
EP + ++LH+D H+++A P L P TP G Y T ++
Sbjct: 30 PDEPPIPFEETILHQD-EHLLVADKPHFL-PV------------TPRGRYVTETLLVRLR 75
Query: 76 QATEPEVLVPISLLHRDNGHVVL 98
+ T L P L R +VL
Sbjct: 76 RQTGNPDLTPAHRLDRLTAGLVL 98
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
0.320 0.140 0.415
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,519,124
Number of extensions: 893749
Number of successful extensions: 779
Number of sequences better than 10.0: 1
Number of HSP's gapped: 769
Number of HSP's successfully gapped: 33
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)