RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= 537021.9.peg.409_1
(242 letters)
>gnl|CDD|31272 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
(contains helicase and exonuclease domains) [DNA
replication, recombination, and repair].
Length = 1139
Score = 134 bits (337), Expect = 3e-32
Identities = 62/207 (29%), Positives = 98/207 (47%), Gaps = 4/207 (1%)
Query: 20 TKSEQLLASDPTRSAWVSANAGSGKTHILVQRVLRLLLA--NAHPSTLLCLTHTKAAAAE 77
T++ Q LAS P +S V A+AG+GKT +L +RVLRLLL +L +T TKAAAAE
Sbjct: 5 TEALQPLASPPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAE 64
Query: 78 MSHRVLEIITAWSHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIH 137
M R+ + + +DE L+++ ++ + +A L LET + TIH
Sbjct: 65 MKERIRDRLKEALQENDEKLASDDELLEALAALIQALIQAIRLFALALETNDEAAIFTIH 124
Query: 138 AFCEAIMQQFPLEANITSHFAIADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILE 197
FC+ I++QF LEA I+ F + ++E L E + EL + ++ +
Sbjct: 125 GFCQRILRQFALEAGISFDFELLEDE--SDLFLELVEDFWRRRFYPLPAELAQLVAQLYK 182
Query: 198 ISNDEDIETLISDIISNRTALKLIFFF 224
+ L+ +I R
Sbjct: 183 FPQATPLPALLLEIELARFGFPAYDLE 209
>gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase. The Rep family
helicases are composed of four structural domains. The
Rep family function as dimers. REP helicases catalyse
ATP dependent unwinding of double stranded DNA to single
stranded DNA. Bacillus subtilis addA and Escherichia
coli exodeoxyribonuclease V beta have large insertions
near to the carboxy-terminus relative to other members
of the family.
Length = 494
Score = 76.2 bits (188), Expect = 7e-15
Identities = 43/176 (24%), Positives = 71/176 (40%), Gaps = 43/176 (24%)
Query: 23 EQLLASDPTRS-AWVSANAGSGKTHILVQRVLRLLLA-NAHPSTLLCLTHTKAAAAEMSH 80
EQ A V A AG+GKT +L +R+ L+L P +L +T T AA EM
Sbjct: 4 EQRKAVTHLGGPLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAREMKE 63
Query: 81 RVLEIITAWSHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFC 140
R+L+++ K S+++ + T H+FC
Sbjct: 64 RILKLL--------------------GKAEASELN-----------------ISTFHSFC 86
Query: 141 EAIMQQFPLEAN-ITSHFAIADEEQSKKLIEEA---KKSTLASIMLDNNEELKKAF 192
I++++ + +F+I DE L++E + L S +L ELK+
Sbjct: 87 LRILRKYANRIGDLLPNFSILDELDQLALLKEILKKDRLDLDSKLLRPLLELKELI 142
>gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA
replication, recombination, and repair].
Length = 655
Score = 62.1 bits (150), Expect = 1e-10
Identities = 44/196 (22%), Positives = 70/196 (35%), Gaps = 40/196 (20%)
Query: 36 VSANAGSGKTHILVQRVLRLLLAN-AHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSD 94
V A AGSGKT +L +R+ L+ A P +L +T T AAAEM R+L+++
Sbjct: 20 VLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG------- 72
Query: 95 EILSAEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFPLEANIT 154
L GL V T H+F I+++ +
Sbjct: 73 ------------------------------LPAAEGLTVGTFHSFALRILRRHGERLGLN 102
Query: 155 SHFAIADEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILEISNDEDIETLISDIISN 214
++F I D + LI+E + L + D ++A I E N S ++
Sbjct: 103 ANFTILDSDDQLALIKELLRREL--NLDDKELLPREALRYISEAKNALLSPLEASALLLA 160
Query: 215 RTALKLIFFFFSYLWR 230
+
Sbjct: 161 AIKSEAEKKLAELYEE 176
>gnl|CDD|37319 KOG2108, KOG2108, KOG2108, 3'-5' DNA helicase [Replication,
recombination and repair].
Length = 853
Score = 31.9 bits (72), Expect = 0.18
Identities = 29/80 (36%), Positives = 36/80 (45%), Gaps = 2/80 (2%)
Query: 18 SQTKSEQLLASDPTRSAWVSANAGSGKTHILVQRVLRLLLANA-HPSTLLCLTHTKAAAA 76
KS++ A P R V A GSGKT +L +RV L+ N P +L T T AA
Sbjct: 13 LLNKSQRFSALSPLRRKRVIAGPGSGKTLVLTERVAYLINFNNIKPDEILINTGTNKAAD 72
Query: 77 EMSHRVLEIITAWSHLSDEI 96
+ L I S S EI
Sbjct: 73 SIKLN-LIAILRTSKCSKEI 91
>gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region..
Length = 144
Score = 31.6 bits (71), Expect = 0.21
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 10/91 (10%)
Query: 41 GSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSDEILSAE 100
GSGKT + +L LL + L L T+ A +++ R+ E+ + I
Sbjct: 10 GSGKTLAALLPILELLDSLKGGQV-LVLAPTRELANQVAERLKEL------FGEGIKVGY 62
Query: 101 ITKIQGKKPNKSDMSKARHLLITILETPGGL 131
+ K + +S +++ TPG L
Sbjct: 63 LIGGTSIKQQEKLLSGKTDIVVG---TPGRL 90
>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 167
Score = 30.3 bits (69), Expect = 0.49
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 36 VSANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEIITAWSHLSDE 95
V A GSGKT + L+ LL N L L T+ A ++ + L+ + + L
Sbjct: 19 VQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQI-YEELKKLGKYLGLKVA 77
Query: 96 ILSAEITKIQGKKPNKSDMSKARHLLITILETPGGL 131
+L + K + K +L+ TPG L
Sbjct: 78 LLYGGDS----PKEQLRKLKKGPDILVG---TPGRL 106
>gnl|CDD|31301 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 29.8 bits (67), Expect = 0.64
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)
Query: 104 IQGKKPNKSDMSKARHLLITILETPGGLKVQTIHAFCEAIMQQFPLEANITSHFAIADEE 163
I+G + K +H++ + +E P ++ Q F + + D E
Sbjct: 78 IKGAALAYRNAQKGKHIITSAIEHPA-----VLNTCRYLERQGFEVTYLPVDSNGLVDLE 132
Query: 164 QSKKLIEEAKKSTLASIMLDNNE 186
Q ++ + + L SIM NNE
Sbjct: 133 QLEEALRP--DTILVSIMHANNE 153
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.4 bits (66), Expect = 0.90
Identities = 39/161 (24%), Positives = 66/161 (40%), Gaps = 23/161 (14%)
Query: 74 AAAEMSHRVLEIITAWSHLSDEILSAEITKIQGKKP-----NKSDMSKARHLLITILETP 128
A E + VL ++ A S D+ A I + KKP NK+D+ + + +
Sbjct: 292 KAIEEADLVLFVLDA-SQPLDKEDLALIELLPKKKPIIVVLNKADLVSK--IELESEKLA 348
Query: 129 GGLKVQTIHA--------FCEAIMQQFPLEANITSHFAIADE------EQSKKLIEEAKK 174
G + +I A EAI Q F +++ EQ+ + +E+A +
Sbjct: 349 NGDAIISISAKTGEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQLLEQAAEHLEDALQ 408
Query: 175 STLASIMLD-NNEELKKAFYEILEISNDEDIETLISDIISN 214
LD E+L+ A + EI+ + E L+ +I SN
Sbjct: 409 QLELGQPLDLLAEDLRLAQEALGEITGEFVSEDLLDEIFSN 449
>gnl|CDD|153178 cd04906, ACT_ThrD-I_1, First of two tandem C-terminal ACT domains
of threonine dehydratase I (ThrD-I; L-threonine
hydrolyase). This CD includes the first of two tandem
C-terminal ACT domains of threonine dehydratase I
(ThrD-I; L-threonine hydrolyase) which catalyzes the
committed step in branched chain amino acid biosynthesis
in plants and microorganisms, the pyridoxal 5'-phosphate
(PLP)-dependent dehydration/deamination of L-threonine
(or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is
a cooperative, feedback-regulated (isoleucine and
valine) allosteric enzyme that forms a tetramer and
contains four pyridoxal phosphate moieties. Members of
this CD belong to the superfamily of ACT regulatory
domains.
Length = 85
Score = 29.1 bits (66), Expect = 1.3
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 18/87 (20%)
Query: 120 LLITILETPGGLKVQTIHAFCEAIMQQFPLEANITS-HFAIADEEQSKKLIE---EAKKS 175
L +TI E PG K FCE I + NIT ++ ADE+ + +
Sbjct: 4 LAVTIPERPGSFK-----KFCELIGPR-----NITEFNYRYADEKDAHIFVGVSVANGAE 53
Query: 176 TLASIMLDNNEELKKAFYEILEISNDE 202
LA ++ E+LK A YE++++S+DE
Sbjct: 54 ELAELL----EDLKSAGYEVVDLSDDE 76
>gnl|CDD|30859 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 28.6 bits (63), Expect = 1.5
Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 9/96 (9%)
Query: 36 VSANAGSGKTHILVQRVLRLLLANAHPSTL--LCLTHTKAAAAEMSHRVLEIITAWSHLS 93
A G+GKT + +L+ +L + + L L T+ A +++ E +
Sbjct: 71 GQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIA----EELRKLGKNL 126
Query: 94 DEILSAEITKIQGKKPNKSDMSKARHLLITILETPG 129
+ A + + + + +++ TPG
Sbjct: 127 GGLRVAVVYGGVSIRKQIEALKRGVDIVV---ATPG 159
>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.7 bits (64), Expect = 1.7
Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 3/89 (3%)
Query: 14 IDLISQTKSEQLLASDPTRSAWVSANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKA 73
IDL+ + L ++SA G G L++ + LL+ L L +T A
Sbjct: 314 IDLLEDEEILAELERGSPNPVFISAKTGEGLD--LLRERIIELLSGLRTEVTLELPYTDA 371
Query: 74 AAAEMSHRVLEIITAWSHLSDEILSAEIT 102
H ++ + D + AE
Sbjct: 372 GRLSWLHDNGIVLEE-EYGEDVRIKAEAP 399
>gnl|CDD|163624 cd07381, MPP_CapA, CapA and related proteins, metallophosphatase
domain. CapA is one of three membrane-associated
enzymes in Bacillus anthracis that is required for
synthesis of gamma-polyglutamic acid (PGA), a major
component of the bacterial capsule. The YwtB and PgsA
proteins of Bacillus subtilis are closely related to
CapA and are also included in this alignment model.
CapA belongs 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 = 239
Score = 28.4 bits (64), Expect = 1.9
Identities = 14/53 (26%), Positives = 17/53 (32%), Gaps = 2/53 (3%)
Query: 122 ITILETPGGLKVQTIHAFCEAIMQQFPLEANITSHFAIADEEQSKKLIEEAKK 174
ILE G+KV A+ D E+ I EAKK
Sbjct: 123 PAILEV-NGIKV-AFLAYTYGTNGIPLAAGARPGGVNPLDLERIAADIAEAKK 173
>gnl|CDD|35553 KOG0332, KOG0332, KOG0332, ATP-dependent RNA helicase [RNA
processing and modification].
Length = 477
Score = 28.0 bits (62), Expect = 2.4
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 5/84 (5%)
Query: 2 IYHNSFQEHSETIDLISQTKSEQLLASDPTRSAWVSANAGSGKTHILVQRVLRLLLANAH 61
+Y FQ+ S+ Q + LL ++P ++ + +G+GKT V +L + +
Sbjct: 105 LYAMKFQKPSKI-----QETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVV 159
Query: 62 PSTLLCLTHTKAAAAEMSHRVLEI 85
+CL T+ A + V E+
Sbjct: 160 VPQCICLAPTRELAPQTGEVVEEM 183
>gnl|CDD|30793 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 316
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 50 QRVLRLL--LANAHPSTLLCLTHTKAAAAEMSHRVL 83
++L LL L + L+ +TH AE++ RV
Sbjct: 190 AQILDLLKELQREKGTALILITHDLGVVAEIADRVA 225
>gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 744
Score = 27.6 bits (61), Expect = 3.3
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 13/118 (11%)
Query: 77 EMSHRVLEIITAWSHLSDEILS-AEITKIQGKKPNKSDMSKARHLLITILETPGGLKVQT 135
++ V+ + W IL ++ Q K +S L+ +LE P G +T
Sbjct: 500 DLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSP------LVSVLLEGPPGSG-KT 552
Query: 136 IHAFCEAIMQQFPLEANITSHFAIADEEQSK-----KLIEEAKKSTLASIMLDNNEEL 188
A A+ FP I+ I E +K K+ E+A KS L+ I++D+ E L
Sbjct: 553 ALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERL 610
>gnl|CDD|110446 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 = 5.4
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 36 VSANAGSGKTHILVQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHR 81
V G GK+ L++++LR L T T K ++ R
Sbjct: 3 VHGVPGCGKST-LIRKLLRTDL-TVIRPTAELRTEGKPDLPNLNVR 46
>gnl|CDD|48537 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain..
Length = 192
Score = 26.7 bits (59), Expect = 5.6
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 161 DEEQSKKLIEEAKKSTLASIMLDNNEELKKAFYEILEISNDE 202
DEE+ + +EE ++ LA + K F E+ EIS +
Sbjct: 53 DEEEDDRFLEEYRRKRLAEM---KALAEKSKFGEVYEISKPD 91
>gnl|CDD|147077 pfam04734, Ceramidase_alk, Neutral/alkaline non-lysosomal
ceramidase. This family represents a group of
neutral/alkaline ceramidases found in both bacteria and
eukaryotes.
Length = 671
Score = 26.8 bits (60), Expect = 5.8
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 8/69 (11%)
Query: 27 ASDP--TRSAWVSANAGSGKTHILVQRVLRLLLANA-----HPSTLLCLTHTKAAAAEMS 79
A +P R +V A+AG + VL L A + L THT A
Sbjct: 45 ADEPNGKRVVFVVADAGMI-FQAVRLGVLERLKARYGDLYTEQNVALSGTHTHAGPGGYL 103
Query: 80 HRVLEIITA 88
H +L IT+
Sbjct: 104 HYLLYQITS 112
>gnl|CDD|31315 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 26.1 bits (57), Expect = 8.2
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 49 VQRVLRLLLANAHPSTLLCLTHTKAAAAEMSHRVLEI 85
++R LR L +T+ +TH + A E++ RV+ +
Sbjct: 176 LRRWLRKLHDRLGVTTVF-VTHDQEEALELADRVVVL 211
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 26.1 bits (58), Expect = 8.8
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 90 SHLSDEILSAEITKIQGKKPNKSDMSKARHLLITILE 126
HL E +S EI +I+G P +S H I +E
Sbjct: 151 GHLPGEKVSPEIARIRGSPPGVGLISPPPHHDIYSIE 187
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
0.317 0.129 0.360
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,739,947
Number of extensions: 132979
Number of successful extensions: 507
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 46
Length of query: 242
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,297,318
Effective search space: 648895018
Effective search space used: 648895018
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: 56 (25.5 bits)