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)