RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780829|ref|YP_003065242.1| ATP-dependent protease ATP-binding subunit [Candidatus Liberibacter asiaticus str. psy62] (437 letters) >gnl|CDD|31413 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]. Length = 444 Score = 589 bits (1521), Expect = e-169 Identities = 255/445 (57%), Positives = 329/445 (73%), Gaps = 16/445 (3%) Query: 6 NFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG 65 +PREIVSELDRYIIGQ +AK+AVAIALRNRWRR QL +LRDE+ PKNIL++GPTGVG Sbjct: 3 EMTPREIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVG 62 Query: 66 KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQ 125 KT I+RRLA+LAGAPFIKVE TKFTE+GYVGR+VE IIRDLV++A+ +VRE + ++V+++ Sbjct: 63 KTEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKLVREEKIEKVKDK 122 Query: 126 ASINAEERILDALVGKT-----------ATSNTREVFRKKLRDGEISDKEIDIEVADTSS 174 A AEERILDALV +S TRE FRKKLR+GE+ DKEI+IEVAD Sbjct: 123 AEELAEERILDALVPPAKNFWGQSENKQESSATREKFRKKLREGELDDKEIEIEVADKGP 182 Query: 175 DISNFDIPG--GASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDT 232 F+I G G NL ++F + G +KKK ++ V++ L+ +E+D+LID + Sbjct: 183 --PGFEIMGPPGMEEMTNNLQDMFGNLGG-KKKKKRKLKVKEAKKLLIEEEADKLIDQEE 239 Query: 233 VHRDSIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSIN 292 + +++I E GIVF+DE DKI R G VSREGVQRDLLPLVEGS+VSTKYG + Sbjct: 240 IKQEAIDAAEQNGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVK 299 Query: 293 TDHILFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKEL 352 TDHILFIASGAFHV++P+DL+PE+QGRFP+RV L +L K DF ILT+ +++LI QYK L Sbjct: 300 TDHILFIASGAFHVAKPSDLIPELQGRFPIRVELDALTKEDFERILTEPKASLIKQYKAL 359 Query: 353 MKTEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTV 412 +KTEG+ L+FT+D+I +A++A +N +IGARRL TV+ER+LEDISF A D+ + V Sbjct: 360 LKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLLEDISFEAPDMSGQKV 419 Query: 413 VIDAEYVRLHIGDFPSETDMYHFIL 437 IDAEYV +GD + D+ FIL Sbjct: 420 TIDAEYVEEKLGDLVANEDLSRFIL 444 >gnl|CDD|35964 KOG0745, KOG0745, KOG0745, Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]. Length = 564 Score = 109 bits (274), Expect = 1e-24 Identities = 75/240 (31%), Positives = 108/240 (45%), Gaps = 70/240 (29%) Query: 245 GIVFLDEFDKIVARDSGNGIG--VSREGVQRDLLPLVEGSSVS--------TKYGS---I 291 GIVFLDE DKI + VS EGVQ+ LL L+EG+ V+ G I Sbjct: 293 GIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQI 352 Query: 292 NTDHILFIASGAF-----HVSR-------------------------------------- 308 +T +ILFIASGAF +SR Sbjct: 353 DTTNILFIASGAFVGLDKIISRRLDDKSLGFGAPSSKGVRANMATKSGVENDAEKRDELL 412 Query: 309 ----PADL-----LPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGII 359 DL +PE GRFPV V L SL++ +LT+ ++ L QYK+L + + Sbjct: 413 EKVESGDLISFGMIPEFVGRFPVLVPLHSLDEDQLVRVLTEPKNALGKQYKKLFGMDNVE 472 Query: 360 LDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDAEYV 419 L FTE +++A+A +A+ + GAR L++++E +L + F K V++D E V Sbjct: 473 LHFTEKALEAIAQLALKRKT-----GARGLRSILESLLLEAMFEVPGSDIKAVLVDEEAV 527 Score = 75.8 bits (186), Expect = 2e-14 Identities = 47/165 (28%), Positives = 77/165 (46%), Gaps = 51/165 (30%) Query: 9 PREIVSELDRYIIGQQDAKRAVAIALRNRWRR---------------------------- 40 P+EI LD++++GQ+ AK+ +++A+ N ++R Sbjct: 136 PKEICEYLDKFVVGQEKAKKVLSVAVYNHYKRIYHNEPSRQKELAEASKSAKDRDNPIEL 195 Query: 41 ------QQLPADLRD------------ELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 Q P + R EL N+LL+GPTG GKT +++ LAR+ PF Sbjct: 196 EISESNAQWPNNQRQIAKALDEDDEDVELEKSNVLLLGPTGSGKTLLAQTLARVLDVPFA 255 Query: 83 KVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRR-----DEV 122 + T T+ GYVG +VE +I+ L+ A V ++++ DEV Sbjct: 256 ICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEV 300 >gnl|CDD|31412 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]. Length = 408 Score = 106 bits (267), Expect = 1e-23 Identities = 70/230 (30%), Positives = 113/230 (49%), Gaps = 61/230 (26%) Query: 245 GIVFLDEFDKIVARDSGNGIG---VSREGVQRDLLPLVEGSSVST-----------KYGS 290 GI+++DE DKI AR S N VS EGVQ+ LL ++EG+ S ++ Sbjct: 164 GIIYIDEIDKI-ARKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPQQEFIQ 222 Query: 291 INTDHILFIASGAF-----HVSR------------------------------PADLL-- 313 ++T +ILFI GAF + + P DL+ Sbjct: 223 VDTSNILFICGGAFAGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPEDLVKF 282 Query: 314 ---PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDAL 370 PE GR PV L+ L++ ILT+ ++ L+ QY++L + +G+ L+FTE+++ A+ Sbjct: 283 GLIPEFIGRLPVIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGVELEFTEEALKAI 342 Query: 371 ADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQE-KTVVIDAEYV 419 A A+ + GAR L++++E +L D+ F L++ + VVI E V Sbjct: 343 AKKAIERKT-----GARGLRSIIEELLLDVMFELPSLEDVEKVVITEEVV 387 Score = 98.7 bits (246), Expect = 3e-21 Identities = 45/104 (43%), Positives = 67/104 (64%), Gaps = 1/104 (0%) Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRD-ELMPKNILLVGPTGVGK 66 +P+EI + LD Y+IGQ+ AK+ +++A+ N ++R D D EL NILL+GPTG GK Sbjct: 51 TPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGK 110 Query: 67 TAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 T +++ LA++ PF + T TE GYVG +VE I+ L+ A Sbjct: 111 TLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAA 154 >gnl|CDD|31416 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 368 Score = 50.7 bits (121), Expect = 7e-07 Identities = 36/109 (33%), Positives = 54/109 (49%), Gaps = 14/109 (12%) Query: 8 SPREIVSELDRYI-----IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPT 62 +PRE E+ I IGQ++AKR + + + P D PKN+L GP Sbjct: 106 TPREEDREIISDITLDDVIGQEEAKRKCRLIME----YLENPERFGD-WAPKNVLFYGPP 160 Query: 63 GVGKTAISRRLARLAGAPFIKVEVTKFTEIG-YVGRNVEQIIRDLVDVA 110 G GKT +++ LA A P + V+ T+ IG +VG + I +L + A Sbjct: 161 GTGKTMMAKALANEAKVPLLLVKATEL--IGEHVGDGARR-IHELYERA 206 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 48.7 bits (116), Expect = 3e-06 Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 17/89 (19%) Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLA--- 77 +GQ++A A+ AL PKN+LL GP G GKT ++R +A Sbjct: 1 VGQEEAIEALREALELP--------------PPKNLLLYGPPGTGKTTLARAIANELFRP 46 Query: 78 GAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106 GAPF+ + + E V + L Sbjct: 47 GAPFLYLNASDLLEGLVVAELFGHFLVRL 75 Score = 30.2 bits (68), Expect = 1.1 Identities = 19/112 (16%), Positives = 42/112 (37%), Gaps = 20/112 (17%) Query: 217 PELMRDESDRLIDMDTVHRDSIQMVE--NYGIVFLDEFDKIVARDSGNGIGVSREGVQRD 274 +L+ + + R ++ E G++F+DE D + G Q Sbjct: 56 SDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL------------SRGAQNA 103 Query: 275 LLPLVEGSSVSTKYGSINTDHILFIASGAFHVSRPADLLPEIQGRFPVRVHL 326 LL ++E + I+ +++ I + + DL + R +R+ + Sbjct: 104 LLRVLETLNDLR----IDRENVRVIGAT--NRPLLGDLDRALYDRLDIRIVI 149 >gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction only]. Length = 329 Score = 47.0 bits (111), Expect = 1e-05 Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 16/84 (19%) Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67 +I SEL++ ++G ++ +AL L ++LL GP GVGKT Sbjct: 14 ILGKIRSELEKVVVGDEEVIELALLAL----------------LAGGHVLLEGPPGVGKT 57 Query: 68 AISRRLARLAGAPFIKVEVTKFTE 91 ++R LAR G PF++++ T Sbjct: 58 LLARALARALGLPFVRIQCTPDLL 81 >gnl|CDD|35953 KOG0734, KOG0734, KOG0734, AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]. Length = 752 Score = 46.9 bits (111), Expect = 1e-05 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 2/59 (3%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 +PK +LLVGP G GKT ++R +A AG PF ++F E+ +VG + +RDL A Sbjct: 336 LPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEM-FVGVGARR-VRDLFAAA 392 >gnl|CDD|35952 KOG0733, KOG0733, KOG0733, Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]. Length = 802 Score = 45.0 bits (106), Expect = 4e-05 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 9/94 (9%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112 P+ +LL GP G GKT+++ +A G PF+ + + G G + E+ IR+L D A + Sbjct: 223 PRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVS-GVSGES-EKKIRELFDQAKS 280 Query: 113 ----IVRESRRDEV---REQASINAEERILDALV 139 IV D + RE+A E RI+ L+ Sbjct: 281 NAPCIVFIDEIDAITPKREEAQREMERRIVAQLL 314 Score = 33.4 bits (76), Expect = 0.11 Identities = 16/33 (48%), Positives = 22/33 (66%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE 85 P +LL GP G GKT +++ +A AGA FI V+ Sbjct: 545 PSGVLLCGPPGCGKTLLAKAVANEAGANFISVK 577 >gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131 Score = 43.7 bits (104), Expect = 1e-04 Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 17/94 (18%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVR 115 +LL GP G GKT +++ +A+ GAPFI++ ++ YVG E+ +R+L + A + Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVG-ESEKRLRELFEAA----K 54 Query: 116 ESRR-----DEV------REQASINAEERILDAL 138 + DE+ R + R+++ L Sbjct: 55 KLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQL 88 Score = 37.2 bits (87), Expect = 0.010 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 13/82 (15%) Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHILFIASGAFH 305 ++F+DE D + G SR V LL ++G + + ++ IA+ Sbjct: 60 VIFIDEIDALAGSRGSGGDSESRR-VVNQLLTELDG-------FTSSLSKVIVIAAT--- 108 Query: 306 VSRPADLLPEI-QGRFPVRVHL 326 +RP L P + +GRF + Sbjct: 109 -NRPDKLDPALLRGRFDRIIEF 129 >gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 386 Score = 43.0 bits (101), Expect = 2e-04 Identities = 20/39 (51%), Positives = 26/39 (66%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91 PK ILL GP G GKT +++ +A+ AGA FI V V+ T Sbjct: 127 PKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTS 165 >gnl|CDD|177080 CHL00176, ftsH, cell division protein; Validated. Length = 638 Score = 42.0 bits (99), Expect = 3e-04 Identities = 17/39 (43%), Positives = 25/39 (64%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91 PK +LLVGP G GKT +++ +A A PF + ++F E Sbjct: 216 PKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVE 254 >gnl|CDD|35950 KOG0731, KOG0731, KOG0731, AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]. Length = 774 Score = 42.0 bits (98), Expect = 3e-04 Identities = 24/54 (44%), Positives = 35/54 (64%), Gaps = 2/54 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106 PK +LLVGP G GKT +++ +A AG PF V ++F E+ +VG + +RDL Sbjct: 344 PKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEM-FVGVGASR-VRDL 395 >gnl|CDD|30672 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]. Length = 308 Score = 41.8 bits (98), Expect = 4e-04 Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 11/101 (10%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVE---VTKFTEIGYVG------RNVEQI 102 PK I++ GPT GKTA++ LA+ G I ++ V + +IG V Sbjct: 2 KPKLIVIAGPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIGTAKPSLEELAGVPHH 61 Query: 103 IRDLVDVAINI-VRESRRDEVREQASINAEERILDALVGKT 142 + D+ D + E +RD + I A ++ LVG T Sbjct: 62 LIDIRDPTESYSAAEFQRDALAAIDDILARGKLP-ILVGGT 101 >gnl|CDD|30813 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]. Length = 596 Score = 41.9 bits (98), Expect = 4e-04 Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%) Query: 51 LMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 +PK +LLVGP G GKT +++ +A AG PF + + F E+ +VG + +RDL + A Sbjct: 181 KIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM-FVGVGASR-VRDLFEQA 238 >gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit [Posttranslational modification, protein turnover, chaperones]. Length = 786 Score = 41.4 bits (97), Expect = 4e-04 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 7/67 (10%) Query: 10 REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPK-NILLVGPTGVGKTA 68 + L + +IGQ +A AV+ A+R + A L D P + L +GPTGVGKT Sbjct: 483 LNLERRLKKRVIGQDEAVEAVSDAIR------RARAGLGDPNRPIGSFLFLGPTGVGKTE 536 Query: 69 ISRRLAR 75 +++ LA Sbjct: 537 LAKALAE 543 Score = 30.7 bits (69), Expect = 0.75 Identities = 13/21 (61%), Positives = 15/21 (71%) Query: 55 NILLVGPTGVGKTAISRRLAR 75 N +LVG GVGKTAI LA+ Sbjct: 193 NPVLVGEPGVGKTAIVEGLAQ 213 >gnl|CDD|36269 KOG1051, KOG1051, KOG1051, Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]. Length = 898 Score = 40.8 bits (95), Expect = 8e-04 Identities = 30/99 (30%), Positives = 50/99 (50%), Gaps = 17/99 (17%) Query: 12 IVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISR 71 + L +IGQ +A A+A A+R + A L+D L +GP GVGKT +++ Sbjct: 556 LEERLHERVIGQDEAVAAIAAAIR------RSRAGLKDPNPDAWFLFLGPDGVGKTELAK 609 Query: 72 RLARL---AGAPFIKVEVTKFTEI--------GYVGRNV 99 LA + FI++++++F E+ GYVG+ Sbjct: 610 ALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEE 648 >gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207 Score = 39.8 bits (94), Expect = 0.001 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 16/54 (29%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73 + GQ+ AKRA+ IA N+L++GP G GKT +++RL Sbjct: 5 VKGQEQAKRALEIAAAGG----------------HNLLMIGPPGSGKTMLAKRL 42 >gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and metabolism]. Length = 172 Score = 39.0 bits (91), Expect = 0.002 Identities = 14/31 (45%), Positives = 18/31 (58%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 NI+L+G G GK+ I R LA+ PFI Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKALNLPFI 31 >gnl|CDD|35948 KOG0729, KOG0729, KOG0729, 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]. Length = 435 Score = 38.8 bits (90), Expect = 0.003 Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 2/58 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 PK +LL GP G GKT +R +A A FI+V ++ + YVG +++R+L ++A Sbjct: 211 PKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSELVQ-KYVGEGA-RMVRELFEMA 266 >gnl|CDD|30812 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]. Length = 494 Score = 38.6 bits (89), Expect = 0.003 Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 2/55 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT--EIGYVGRNVEQIIRD 105 PK +LL GP G GKT +++ +A + + FI V+ ++ +G +N+ ++ Sbjct: 276 PKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEK 330 >gnl|CDD|31415 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]. Length = 406 Score = 37.5 bits (87), Expect = 0.007 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 2/58 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 PK +LL GP G GKT +++ +A A FI+V ++ + Y+G +++R+L ++A Sbjct: 185 PKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQ-KYIGEG-ARLVRELFELA 240 Score = 28.7 bits (64), Expect = 3.0 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%) Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLV 279 I+F+DE D I A+ +G RE VQR +L L+ Sbjct: 247 IIFIDEIDAIGAKRFDSGTSGDRE-VQRTMLELL 279 >gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.. Length = 154 Score = 37.5 bits (87), Expect = 0.007 Identities = 14/28 (50%), Positives = 19/28 (67%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFI 82 NI+L+G G GKT + R LA+ G PF+ Sbjct: 1 NIVLIGMMGAGKTTVGRLLAKALGLPFV 28 >gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]. Length = 403 Score = 36.9 bits (85), Expect = 0.010 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 16/87 (18%) Query: 9 PREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTA 68 + SE +IG+ + + + R+Q+ A L +L++G TG GK Sbjct: 69 RPYLKSEALDDLIGESPSLQEL---------REQIKAYAPSGL---PVLIIGETGTGKEL 116 Query: 69 ISRRL----ARLAGAPFIKVEVTKFTE 91 +R + AR A APFI ++E Sbjct: 117 FARLIHALSARRAEAPFIAFNCAAYSE 143 >gnl|CDD|35946 KOG0727, KOG0727, KOG0727, 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]. Length = 408 Score = 36.9 bits (85), Expect = 0.011 Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 7/90 (7%) Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAP 80 + +Q+ + AV + L + +Q+ D P+ +LL GP G GKT +++ +A A Sbjct: 162 VQKQEIREAVELPLTHADLYKQIGID-----PPRGVLLYGPPGTGKTMLAKAVANHTTAA 216 Query: 81 FIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 FI+V ++F + Y+G +++RD+ +A Sbjct: 217 FIRVVGSEFVQ-KYLGEG-PRMVRDVFRLA 244 >gnl|CDD|177027 CHL00095, clpC, Clp protease ATP binding subunit. Length = 821 Score = 36.2 bits (84), Expect = 0.019 Identities = 32/99 (32%), Positives = 50/99 (50%), Gaps = 21/99 (21%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73 L + IIGQ +A AV+ A+R R R L++ P + L GPTGVGKT +++ L Sbjct: 506 TLHKRIIGQDEAVVAVSKAIR-RAR-----VGLKNPNRPIASFLFSGPTGVGKTELTKAL 559 Query: 74 ARL---AGAPFIKVEVTKFTE-----------IGYVGRN 98 A + I+++++++ E GYVG N Sbjct: 560 ASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYN 598 Score = 28.9 bits (65), Expect = 2.6 Identities = 12/22 (54%), Positives = 16/22 (72%) Query: 55 NILLVGPTGVGKTAISRRLARL 76 N +L+G GVGKTAI+ LA+ Sbjct: 202 NPILIGEPGVGKTAIAEGLAQR 223 >gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]. Length = 782 Score = 35.9 bits (83), Expect = 0.020 Identities = 14/40 (35%), Positives = 25/40 (62%) Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 L +L + LVGP GVGKT++ + +A+ G F+++ + Sbjct: 344 LTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISL 383 >gnl|CDD|35949 KOG0730, KOG0730, KOG0730, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 693 Score = 36.1 bits (83), Expect = 0.020 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 PK +LL GP G GKT +++ LA AG F+ V+ + YVG + E+ IR++ A Sbjct: 468 PKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELF-SKYVGES-ERAIREVFRKA 523 Score = 31.4 bits (71), Expect = 0.50 Identities = 13/34 (38%), Positives = 18/34 (52%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 P+ +LL GP G GKT + R +A GA + Sbjct: 218 PRGLLLYGPPGTGKTFLVRAVANEYGAFLFLING 251 >gnl|CDD|143926 pfam00158, Sigma54_activat, Sigma-54 interaction domain. Length = 168 Score = 35.8 bits (84), Expect = 0.023 Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 3/35 (8%) Query: 53 PKNILLVGPTGVGKTAISRRLARL---AGAPFIKV 84 +L+ G +G GK +R + +L A PF+ V Sbjct: 22 DATVLITGESGTGKELFARAIHQLSPRADGPFVAV 56 >gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]. Length = 906 Score = 35.7 bits (82), Expect = 0.023 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 8/74 (10%) Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG--------YVGRN 98 LR + K + VGP GVGKT+I++ +AR F + V T++ YVG Sbjct: 432 LRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAM 491 Query: 99 VEQIIRDLVDVAIN 112 +II+ L V Sbjct: 492 PGKIIQCLKKVKTE 505 >gnl|CDD|177097 CHL00206, ycf2, Ycf2; Provisional. Length = 2281 Score = 35.7 bits (82), Expect = 0.026 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%) Query: 44 PADLRDELMP-KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKF 89 P LR L P + IL++G G G++ + + LA + PFI V + KF Sbjct: 1620 PFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKF 1666 >gnl|CDD|35871 KOG0652, KOG0652, KOG0652, 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]. Length = 424 Score = 35.0 bits (80), Expect = 0.047 Identities = 37/132 (28%), Positives = 60/132 (45%), Gaps = 22/132 (16%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112 PK +L+ GP G GKT ++R A A F+K+ + ++ ++G +++RD A Sbjct: 205 PKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQM-FIGDGA-KLVRD----AFA 258 Query: 113 IVRESRRDEVREQASINAEERILDALVGK---TATSNTREVFRKKLR-----DGEISDKE 164 + +E + I +E LDA+ K + + REV R L DG SD Sbjct: 259 LAKE------KAPTIIFIDE--LDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDR 310 Query: 165 IDIEVADTSSDI 176 + + A DI Sbjct: 311 VKVIAATNRVDI 322 >gnl|CDD|35870 KOG0651, KOG0651, KOG0651, 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]. Length = 388 Score = 34.9 bits (80), Expect = 0.048 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIRDLVDVA 110 PK +LL GP G GKT ++R +A G F+KV + + IG R + + R +V Sbjct: 166 PKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMFRYAREVI 225 Query: 111 INIVRESRRDEV 122 I+ D + Sbjct: 226 PCIIFMDEIDAI 237 >gnl|CDD|35959 KOG0740, KOG0740, KOG0740, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 428 Score = 34.6 bits (79), Expect = 0.057 Identities = 30/96 (31%), Positives = 49/96 (51%), Gaps = 14/96 (14%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELM-----PKNILLVGPTGVGKTAISRRLA 74 I G +DAK+++ A+ LP D + + +LL GP G GKT +++ +A Sbjct: 155 IAGLEDAKQSLKEAV-------ILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIA 207 Query: 75 RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 +GA F + + T YVG + E+++R L VA Sbjct: 208 TESGATFFNISASSLTS-KYVGES-EKLVRALFKVA 241 >gnl|CDD|35954 KOG0735, KOG0735, KOG0735, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 952 Score = 34.2 bits (78), Expect = 0.068 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 6/61 (9%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI--GYVGRNVEQIIRDLVDV 109 + ILL GP G GKT ++ +A + FI V K E+ Y+G + EQ +RDL + Sbjct: 700 LRTGILLYGPPGCGKTLLASAIASNSNLRFISV---KGPELLSKYIGAS-EQNVRDLFER 755 Query: 110 A 110 A Sbjct: 756 A 756 Score = 27.3 bits (60), Expect = 9.2 Identities = 11/24 (45%), Positives = 13/24 (54%) Query: 51 LMPKNILLVGPTGVGKTAISRRLA 74 NILL GP G GKT + + L Sbjct: 429 FRHGNILLNGPKGSGKTNLVKALF 452 >gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]. Length = 436 Score = 34.4 bits (79), Expect = 0.068 Identities = 11/36 (30%), Positives = 18/36 (50%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90 +++L GP G GKT ++R +A A F + Sbjct: 50 SMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSG 85 >gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 744 Score = 34.2 bits (78), Expect = 0.070 Identities = 13/29 (44%), Positives = 21/29 (72%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKV 84 +LL GP G GKTA++ ++A + PF+K+ Sbjct: 541 VLLEGPPGSGKTALAAKIALSSDFPFVKI 569 Score = 30.7 bits (69), Expect = 0.74 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 5/55 (9%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI--GYVGRNVEQIIRDL 106 K ILL GP G GKT I+R++ ++ A K + EI YVG + E+ +R L Sbjct: 257 KGILLYGPPGTGKTLIARQIGKMLNAREPK--IVNGPEILNKYVGES-EENVRKL 308 >gnl|CDD|35957 KOG0738, KOG0738, KOG0738, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 491 Score = 34.2 bits (78), Expect = 0.071 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 2/57 (3%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 K +L+VGP G GKT +++ +A G F V + T + G + E+++R L ++A Sbjct: 246 KGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTS-KWRGES-EKLVRLLFEMA 300 >gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]. Length = 490 Score = 34.0 bits (78), Expect = 0.078 Identities = 25/77 (32%), Positives = 32/77 (41%), Gaps = 25/77 (32%) Query: 9 PREIVSELDRY---------IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLV 59 P I SE+ + GQ+ AKRA+ IA N+LLV Sbjct: 161 PIPIPSEVIESFSLAPDFKDVKGQEQAKRALEIAAAGG----------------HNLLLV 204 Query: 60 GPTGVGKTAISRRLARL 76 GP G GKT ++ RL L Sbjct: 205 GPPGTGKTMLASRLPGL 221 >gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid. Length = 232 Score = 33.9 bits (78), Expect = 0.086 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 57 LLVGPTGVGKTAISRRLARLAGAPFI 82 L+ G T GKTA + LA+ G P I Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVI 30 >gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.. Length = 150 Score = 33.3 bits (76), Expect = 0.12 Identities = 12/27 (44%), Positives = 19/27 (70%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82 I+++G +G GK+ + + LA GAPFI Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28 >gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.. Length = 194 Score = 32.5 bits (74), Expect = 0.23 Identities = 36/127 (28%), Positives = 58/127 (45%), Gaps = 22/127 (17%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIR--DL 106 ILL+GP G GK + RLA+ G P I E+ TE+ G+ ++ I L Sbjct: 1 RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLREEIASGTEL---GKKAKEYIDSGKL 57 Query: 107 V--DVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKE 164 V ++ I +++E + ++ ILD G T + E + L +G DK Sbjct: 58 VPDEIVIKLLKERLKKPDCKKGF------ILD---GFPRTVDQAEALDELLDEGIKPDKV 108 Query: 165 IDIEVAD 171 I+++V D Sbjct: 109 IELDVPD 115 >gnl|CDD|31609 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]. Length = 407 Score = 32.6 bits (74), Expect = 0.25 Identities = 15/26 (57%), Positives = 17/26 (65%), Gaps = 3/26 (11%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAG 78 + I LVGPTGVGKT LA+LA Sbjct: 203 KRVIALVGPTGVGKTTT---LAKLAA 225 >gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 322 Score = 32.3 bits (73), Expect = 0.25 Identities = 33/171 (19%), Positives = 63/171 (36%), Gaps = 22/171 (12%) Query: 52 MPKNILLVGPTGVGKT----AISRRLARLAGAPFIKVEVTKFTEIGYV-----GRNVEQI 102 M + + G GVGKT A + +LA +G + V +G V G + ++ Sbjct: 1 MTRIVFFTGKGGVGKTTIAAATAVKLAE-SGKKVLLVSTDPAHSLGDVFDLELGHDPRKV 59 Query: 103 IRDLVDVAINIVRESRR--DEVREQASINAEERILDALVGKTATS--NTREVFRKKLRDG 158 +L + ++ + DEV++ + R L + + E Sbjct: 60 GPNLDALELDPEKALEEYWDEVKDYLARLLRTRGLGGIYADELATLPGIDEALALLKILE 119 Query: 159 EISDKEIDIEVADTSSDISNFDIPGGASVGILNLSELFSKVMGSGRKKKIR 209 E D+ V DT+ P G ++ +L+L E+ + K + + Sbjct: 120 YYVSGEYDVIVVDTA--------PTGHTLRLLSLPEVLGWYLEKLFKPRRK 162 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 32.4 bits (73), Expect = 0.25 Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 6/114 (5%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIV 114 IL+ GPTG GKT ++ +LA KV E + I+ Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60 Query: 115 RESRRDEVREQASINAEERILDA------LVGKTATSNTREVFRKKLRDGEISD 162 + D+ ++ ER+ + ++ + ++ GE+ + Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDE 114 >gnl|CDD|35947 KOG0728, KOG0728, KOG0728, 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]. Length = 404 Score = 32.3 bits (73), Expect = 0.28 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 2/58 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 PK +LL GP G GKT ++R +A FI+V ++ + Y+G +++R+L +A Sbjct: 181 PKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQ-KYIGEG-SRMVRELFVMA 236 >gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]. Length = 366 Score = 32.3 bits (73), Expect = 0.29 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%) Query: 49 DELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108 P NI++ GPTG GKTA + + VEV + R Q++ +++ Sbjct: 38 RGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLEL--RTPYQVLSKILN 95 Query: 109 VAINI 113 + Sbjct: 96 KLGKV 100 >gnl|CDD|35961 KOG0742, KOG0742, KOG0742, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 630 Score = 32.3 bits (73), Expect = 0.29 Identities = 35/141 (24%), Positives = 57/141 (40%), Gaps = 20/141 (14%) Query: 54 KNILLVGPTGVGKTAISRRLARLAG-----------APFIKVEVTKFTEIGYVGRNVEQI 102 +NIL GP G GKT +R LAR +G AP VTK ++ + + Sbjct: 385 RNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRG 444 Query: 103 IRDLVDVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISD 162 + +D A + E + + E A+ L+AL+ +T + V Sbjct: 445 LLLFIDEADAFLCERNKTYMSE-----AQRSALNALLFRTGDQSRDIVLVLATNRPG--- 496 Query: 163 KEIDIEVADTSSDISNFDIPG 183 ++D V D ++ F +PG Sbjct: 497 -DLDSAVNDRIDEVVEFPLPG 516 >gnl|CDD|37239 KOG2028, KOG2028, KOG2028, ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]. Length = 554 Score = 32.0 bits (72), Expect = 0.30 Identities = 24/108 (22%), Positives = 45/108 (41%), Gaps = 18/108 (16%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74 LD Y+ GQ + LR+ + ++P+ ++L GP G GKT ++R +A Sbjct: 136 TLDDYV-GQSHLVGQDGL-LRSLIEQNRIPS----------MILWGPPGTGKTTLARLIA 183 Query: 75 RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEV 122 + +F E+ +RD+ + A N ++R + Sbjct: 184 STSKKHSY-----RFVELSATNAKTND-VRDIFEQAQNEKSLTKRKTI 225 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 32.0 bits (74), Expect = 0.33 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDL 106 I + G +G GKT + +AR A A ++V + IG GR V + I +L Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV----YVLIGERGREVAEFIEEL 64 >gnl|CDD|37381 KOG2170, KOG2170, KOG2170, ATPase of the AAA+ superfamily [General function prediction only]. Length = 344 Score = 31.8 bits (72), Expect = 0.37 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 13/64 (20%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLV---GPTGVGKTAISR 71 +L R + GQ AK+ V AL++ W P+ L++ G TG GK ++ Sbjct: 79 DLARALFGQHLAKQLVVNALKSHWANPN----------PRKPLVLSFHGWTGTGKNYVAE 128 Query: 72 RLAR 75 +A Sbjct: 129 IIAE 132 >gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription]. Length = 450 Score = 31.8 bits (72), Expect = 0.38 Identities = 32/116 (27%), Positives = 54/116 (46%), Gaps = 28/116 (24%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRLAR--- 75 ++GQ++A+ A + ++ ++ M + IL+VGP G GKTA++ +AR Sbjct: 41 LVGQEEAREAAGVIVKM----------IKQGKMAGRGILIVGPPGTGKTALAMGIARELG 90 Query: 76 -------LAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVRE 124 ++G+ +EV K TE + Q +R + V I RE EV E Sbjct: 91 EDVPFVAISGSEIYSLEVKK-TEA------LTQALRRAIGVRIKETREVYEGEVVE 139 >gnl|CDD|35945 KOG0726, KOG0726, KOG0726, 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]. Length = 440 Score = 31.8 bits (72), Expect = 0.39 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIRDLVDVA 110 PK ++L G G GKT +++ +A A F++V ++ + +G + V ++ R + A Sbjct: 219 PKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHA 278 Query: 111 INIV 114 +IV Sbjct: 279 PSIV 282 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 31.8 bits (72), Expect = 0.42 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 2/71 (2%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVR 115 I +VGP G GK+ + + LA G V+V + +IGY ++ +++ D + + Sbjct: 351 IAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDEL--DPDKTVLEELS 408 Query: 116 ESRRDEVREQA 126 E D ++ Sbjct: 409 EGFPDGDEQEV 419 >gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]. Length = 4600 Score = 31.6 bits (71), Expect = 0.44 Identities = 18/46 (39%), Positives = 28/46 (60%) Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEI 92 LR + K ILL G GVGKT++ LAR G I++ +++ T++ Sbjct: 1537 LRAMQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDL 1582 Score = 30.8 bits (69), Expect = 0.71 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 3/56 (5%) Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93 W +QL +++ + LLVG TG GKT + + LA + ++ TE+ Sbjct: 452 WLLEQLLWNIQ---NNEPTLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQTEMS 504 Score = 29.3 bits (65), Expect = 2.0 Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 1/42 (2%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG-YVG 96 +L+ GPT GKT++ LAR G F+++ + T++ Y+G Sbjct: 891 LLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIG 932 Score = 28.9 bits (64), Expect = 2.7 Identities = 13/24 (54%), Positives = 18/24 (75%) Query: 56 ILLVGPTGVGKTAISRRLARLAGA 79 ++LVG TGVGKT++ R LA + G Sbjct: 1853 LILVGDTGVGKTSLLRFLASIFGQ 1876 >gnl|CDD|133262 cd01853, Toc34_like, Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon. Length = 249 Score = 31.5 bits (72), Expect = 0.48 Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%) Query: 42 QLPADLRDELMPK-NILLVGPTGVGKTAI 69 +L A ++EL IL++G TGVGK++ Sbjct: 19 ELEAKGKEELDFSLTILVLGKTGVGKSST 47 >gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]. Length = 176 Score = 31.4 bits (71), Expect = 0.55 Identities = 12/30 (40%), Positives = 19/30 (63%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV 84 NIL+ G G GK+ ++ RLA G +I++ Sbjct: 9 NILVTGTPGTGKSTLAERLAEKTGLEYIEI 38 >gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins. Length = 196 Score = 31.4 bits (72), Expect = 0.56 Identities = 12/24 (50%), Positives = 13/24 (54%) Query: 53 PKNILLVGPTGVGKTAISRRLARL 76 P ILLVG G GKT +LA Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAY 24 >gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.. Length = 287 Score = 31.3 bits (71), Expect = 0.57 Identities = 12/30 (40%), Positives = 18/30 (60%) Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLA 74 +LR+ L K +LVG +GVGK+ + L Sbjct: 153 DELREYLKGKTSVLVGQSGVGKSTLINALL 182 >gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.. Length = 147 Score = 31.3 bits (71), Expect = 0.58 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 9/68 (13%) Query: 60 GPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQI--IRDLVDVAI------ 111 GP G GK+ +++ LA+ G P++ + E+G + V I +R +D Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLDTGGIRTEEVGKLASEVAAIPEVRKALDERQRELAKK 65 Query: 112 -NIVRESR 118 IV E R Sbjct: 66 PGIVLEGR 73 >gnl|CDD|29833 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.. Length = 149 Score = 31.0 bits (70), Expect = 0.60 Identities = 22/127 (17%), Positives = 53/127 (41%), Gaps = 8/127 (6%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG--YVGRNVEQIIRDLVDV---- 109 +L+ GP+G+GK+ ++ L + G + + G VGR E ++ L+++ Sbjct: 17 VLITGPSGIGKSELALELIK-RGHRLVADDRVVVKREGGRLVGRAPE-ALKGLIEIRGLG 74 Query: 110 AINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEV 169 I++ R + VR++ I+ + + K E K++ ++ + + Sbjct: 75 IIDVPRLYGIEAVRDRKVIDLVIELEEWEEEKNFDRLGLEEEYKRILGVKVPLLRLPVSP 134 Query: 170 ADTSSDI 176 + + Sbjct: 135 GRNLAVL 141 >gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. Length = 103 Score = 31.0 bits (71), Expect = 0.65 Identities = 11/31 (35%), Positives = 14/31 (45%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKV 84 K L+V TG GKT + +L KV Sbjct: 19 KRGLIVMATGSGKTLTAAKLIARLLKGKKKV 49 >gnl|CDD|36760 KOG1547, KOG1547, KOG1547, Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms, Cytoskeleton]. Length = 336 Score = 30.7 bits (69), Expect = 0.79 Identities = 22/109 (20%), Positives = 44/109 (40%), Gaps = 24/109 (22%) Query: 55 NILLVGPTGVGKTAI-----SRRLARLAGAPFIKVEVTKFTEIGYVGRNVE----QIIRD 105 NI++VG +G+GK+ + ++ + + + K TEI + +E ++ Sbjct: 48 NIMVVGQSGLGKSTLINTLFKSHVSDSSSSDNSAEPIPKTTEIKSITHVIEEKGVKLKLT 107 Query: 106 LVDVA---------------INIVRESRRDEVREQASINAEERILDALV 139 ++D + E +RE+ +I E+RI D V Sbjct: 108 VIDTPGFGDQINNDNCWEPIEKYINEQYEQYLREELNIAREKRIPDTRV 156 >gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. Length = 159 Score = 30.5 bits (70), Expect = 0.86 Identities = 9/18 (50%), Positives = 14/18 (77%) Query: 56 ILLVGPTGVGKTAISRRL 73 I+L+G +GVGKT++ R Sbjct: 3 IVLIGDSGVGKTSLLLRF 20 >gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Length = 122 Score = 30.4 bits (69), Expect = 1.1 Identities = 13/38 (34%), Positives = 19/38 (50%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93 +L+VGP GKT + R+L +V V K + G Sbjct: 3 VLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHG 40 >gnl|CDD|32436 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]. Length = 332 Score = 30.1 bits (68), Expect = 1.1 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 9/55 (16%) Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 IGQ+ K + I ++ A R E ++LL GP G+GKT ++ +A Sbjct: 29 IGQEKVKEQLQIFIK--------AAKKRGE-ALDHVLLFGPPGLGKTTLAHIIAN 74 >gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]. Length = 299 Score = 30.2 bits (68), Expect = 1.2 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 6/38 (15%) Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 WRR +R P IL+ G +GVGK+ I+ LAR Sbjct: 80 WRR------IRKMKRPLIILIGGASGVGKSTIAGELAR 111 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 30.2 bits (69), Expect = 1.2 Identities = 10/30 (33%), Positives = 16/30 (53%) Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLA 74 +L+ L K +L G +GVGK+ + L Sbjct: 27 EELKPLLKGKTSVLAGQSGVGKSTLLNALL 56 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 29.9 bits (67), Expect = 1.3 Identities = 10/34 (29%), Positives = 17/34 (50%) Query: 41 QQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74 +L + L K +L+G +GVGK+ + L Sbjct: 152 GDGLEELAELLAGKITVLLGQSGVGKSTLINALL 185 >gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]. Length = 935 Score = 30.0 bits (67), Expect = 1.3 Identities = 34/173 (19%), Positives = 63/173 (36%), Gaps = 29/173 (16%) Query: 57 LLVGPTGVGKT----AISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAIN 112 L+ GP G GKT I LAR P + + V+Q+ + + Sbjct: 429 LIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIA--------VDQLAEKIHKTGLK 480 Query: 113 IVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEVADT 172 +VR + RE + L + +++ + K GE+S + Sbjct: 481 VVRLCAKS--REDIESDVSFLSLHEQLRNMDKPELQKLLKLKDEGGELSSSD-------- 530 Query: 173 SSDISNFDIPGGASVGILNLSE-LFSKVMGSGRKKKIRMSVQKCYPELMRDES 224 + + A +LN ++ + +G+G + R+S K L+ DE+ Sbjct: 531 --EKKYRKLKRAAEKELLNQADVICCTCVGAGDR---RLSKFKFRTVLI-DEA 577 >gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]. Length = 464 Score = 29.9 bits (67), Expect = 1.3 Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 14/96 (14%) Query: 3 LTFNFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPA------DLRDEL----- 51 L F +++ ++R + ++ + R + +L LR + Sbjct: 103 LEKPFDLDRLLAIVERALELRELQRENRRSLKRAKSLGGELVGESPAMQQLRRLIAKVAP 162 Query: 52 MPKNILLVGPTGVGKTAISR---RLARLAGAPFIKV 84 ++L+ G +G GK ++R + + A PFI V Sbjct: 163 SDASVLITGESGTGKELVARAIHQASPRAKGPFIAV 198 >gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA replication, recombination, and repair]. Length = 325 Score = 29.9 bits (66), Expect = 1.3 Identities = 13/36 (36%), Positives = 19/36 (52%) Query: 40 RQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 ++ L L +P +L GP GVGKT + LA+ Sbjct: 11 KRLLVQALESGRLPHALLFYGPPGVGKTTAALALAK 46 >gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. Length = 178 Score = 29.9 bits (68), Expect = 1.3 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 55 NILLVGPTGVGKTAISRRLARLA 77 N+LL+GP GVGKT ++ L A Sbjct: 49 NLLLLGPPGVGKTHLACALGHQA 71 >gnl|CDD|30990 COG0645, COG0645, Predicted kinase [General function prediction only]. Length = 170 Score = 29.9 bits (67), Expect = 1.4 Identities = 12/31 (38%), Positives = 20/31 (64%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 +L+ G G GK+ ++R LA L GA ++ +V Sbjct: 4 VLVGGLPGSGKSTLARGLAELLGAIRLRSDV 34 >gnl|CDD|35955 KOG0736, KOG0736, KOG0736, Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]. Length = 953 Score = 30.0 bits (67), Expect = 1.5 Identities = 12/35 (34%), Positives = 19/35 (54%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90 +LL GP G GKT + R +A G ++V+ + Sbjct: 434 VLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELV 468 >gnl|CDD|132912 cd07041, STAS_RsbR_RsbS_like, Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors. Length = 109 Score = 29.7 bits (68), Expect = 1.6 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 4/35 (11%) Query: 381 VGDIGARRLQTVMERVLEDISFSASDLQEKTVVID 415 +GD+ R + + ER+LE I S + + V+ID Sbjct: 17 IGDLDDERAEQLQERLLEAI----SRRRARGVIID 47 >gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria [Function unknown]. Length = 308 Score = 29.6 bits (66), Expect = 1.6 Identities = 12/22 (54%), Positives = 16/22 (72%) Query: 55 NILLVGPTGVGKTAISRRLARL 76 N L++GP VGKT + R +ARL Sbjct: 139 NTLIIGPPQVGKTTLLRDIARL 160 >gnl|CDD|37180 KOG1969, KOG1969, KOG1969, DNA replication checkpoint protein CHL12/CTF18 [Energy production and conversion, Replication, recombination and repair]. Length = 877 Score = 29.6 bits (66), Expect = 1.6 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%) Query: 38 WRRQQLPADLRDELMP--KNILLVGPTGVGKTAISRRLARLAG 78 ++ L +L P K +LL GP G+GKT ++ +A+ AG Sbjct: 309 TEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTLAHVIAKQAG 351 >gnl|CDD|30631 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 222 Score = 29.8 bits (67), Expect = 1.7 Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 20/110 (18%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI----------------KVEVTKFTEIGYV 95 I + GP G GK+ +++ LA G ++ V++ + + Sbjct: 3 AAIIIAIDGPAGSGKSTVAKILAEKLGFHYLDTGAMYRAVALAALKHGVDLDDEDALVAL 62 Query: 96 GRNVEQIIRDLVDVAIN---IVRESRRDEVREQAS-INAEERILDALVGK 141 + ++ + V +N + E R +EV AS + A + +ALV Sbjct: 63 AKELDISFVNDDRVFLNGEDVSEEIRTEEVGNAASKVAAIPEVREALVKL 112 >gnl|CDD|34269 COG4650, RtcR, Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]. Length = 531 Score = 29.6 bits (66), Expect = 1.8 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 26/86 (30%) Query: 25 DAKRAVAIALRNRWRRQQLPADLRDELMPKN--------------------ILLVGPTGV 64 D R AIA R R+Q L+ + +N ILL GPTG Sbjct: 160 DLSRYNAIASRFAEEREQTLDFLKSGIATRNPHFNRMIEQIERVAIRSRAPILLNGPTGA 219 Query: 65 GKTAISRRLARLAGA------PFIKV 84 GK+ ++RR+ L A F++V Sbjct: 220 GKSFLARRIYELKQARHQFSGAFVEV 245 >gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. Length = 165 Score = 29.6 bits (67), Expect = 1.9 Identities = 9/25 (36%), Positives = 14/25 (56%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAP 80 ++L G G GKT + ++LA L Sbjct: 3 VILQGEAGSGKTTLLQKLALLWAQG 27 >gnl|CDD|112109 pfam03279, Lip_A_acyltrans, Bacterial lipid A biosynthesis acyltransferase. Length = 295 Score = 29.6 bits (67), Expect = 1.9 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 9/50 (18%) Query: 200 MGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIVFL 249 G R+K R ++ C+PE+ E +++ID Q + ++G+ L Sbjct: 48 FGKRRRKIARKNLALCFPEMSEAEREKIID---------QSLASFGMAIL 88 >gnl|CDD|38288 KOG3078, KOG3078, KOG3078, Adenylate kinase [Nucleotide transport and metabolism]. Length = 235 Score = 29.5 bits (66), Expect = 2.0 Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 6/57 (10%) Query: 43 LPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIG 93 P DE +L+G G GK + RL + G I E+ TE+G Sbjct: 5 APGFDEDEKKGVRAVLLGAPGSGKGTQAPRLTKNFGVIHISTGDLLRDEIASGTELG 61 >gnl|CDD|146942 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. Length = 200 Score = 29.5 bits (67), Expect = 2.0 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 54 KNILLVGPTGVGKTA 68 I+LVG TG GK+A Sbjct: 1 LRIVLVGKTGNGKSA 15 >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 = 29.1 bits (66), Expect = 2.4 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 51 LMPKNILLVGPTGVGKTAI 69 L K++L+ PTG GKT Sbjct: 12 LEGKDVLVQAPTGSGKTLA 30 >gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]. Length = 442 Score = 28.9 bits (64), Expect = 2.6 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%) Query: 27 KRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 A LR ++ + L A +++ + ++V PTG GKT ++ + + Sbjct: 30 IVAFEFELRP-YQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLVP 88 Query: 87 TK 88 TK Sbjct: 89 TK 90 >gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. Length = 105 Score = 29.1 bits (66), Expect = 2.7 Identities = 10/20 (50%), Positives = 14/20 (70%) Query: 56 ILLVGPTGVGKTAISRRLAR 75 I L GP G GK+ +++ LAR Sbjct: 1 IWLYGPPGCGKSTLAKYLAR 20 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 29.1 bits (65), Expect = 2.7 Identities = 11/29 (37%), Positives = 20/29 (68%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFI 82 IL++GP G GK+ ++++LA+ G P + Sbjct: 1 MRILILGPPGAGKSTLAKKLAKKLGLPHL 29 >gnl|CDD|33076 COG3265, GntK, Gluconate kinase [Carbohydrate transport and metabolism]. Length = 161 Score = 29.1 bits (65), Expect = 2.8 Identities = 10/23 (43%), Positives = 13/23 (56%) Query: 60 GPTGVGKTAISRRLARLAGAPFI 82 G +G GK+ + LA GA FI Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24 >gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]. Length = 180 Score = 28.7 bits (64), Expect = 2.9 Identities = 9/24 (37%), Positives = 12/24 (50%) Query: 54 KNILLVGPTGVGKTAISRRLARLA 77 I + G GVGKT + + L L Sbjct: 1 MLIAITGTPGVGKTTVCKLLRELG 24 >gnl|CDD|73180 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.. Length = 137 Score = 29.0 bits (65), Expect = 2.9 Identities = 10/18 (55%), Positives = 15/18 (83%) Query: 56 ILLVGPTGVGKTAISRRL 73 I+L GP+GVGK+ + +RL Sbjct: 2 IVLSGPSGVGKSTLLKRL 19 >gnl|CDD|147593 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 234 Score = 29.0 bits (66), Expect = 2.9 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 10/66 (15%) Query: 16 LDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 LD YI GQ+ K + I + A R E + ++LL GP G+GKT ++ +A Sbjct: 23 LDEYI-GQEKVKENLKIFIE--------AAKKRGEAL-DHVLLYGPPGLGKTTLANIIAN 72 Query: 76 LAGAPF 81 G Sbjct: 73 EMGVNI 78 >gnl|CDD|31198 COG0857, Pta, BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]. Length = 354 Score = 28.7 bits (64), Expect = 3.1 Identities = 31/141 (21%), Positives = 51/141 (36%), Gaps = 19/141 (13%) Query: 52 MPKNILLVGP-TGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 M + +LL+ TGVGKT+IS L R +KV K I A Sbjct: 1 MSRTLLLIPTETGVGKTSISLGLLRALEQKGLKVAYFK------------PIGTRTGKDA 48 Query: 111 INIVRESRRDEVREQASIN-AEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDIEV 169 ++ E D +S+ AE +L +T + + L + K+ D+ V Sbjct: 49 DDLTEE---DIRATSSSLTYAEPLVLSFAEVLLSTGQDDVLLEEILANYAELAKDADVVV 105 Query: 170 ADTSSDISNFDIPGGASVGIL 190 + D+ + P + Sbjct: 106 VE--GDVPTREGPYALDLNYE 124 >gnl|CDD|133313 cd04113, Rab4, Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 28.8 bits (65), Expect = 3.2 Identities = 5/18 (27%), Positives = 11/18 (61%) Query: 56 ILLVGPTGVGKTAISRRL 73 +++G +G GK+ + R Sbjct: 3 FIIIGSSGTGKSCLLHRF 20 >gnl|CDD|35305 KOG0082, KOG0082, KOG0082, G-protein alpha subunit (small G protein superfamily) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 354 Score = 28.6 bits (64), Expect = 3.4 Identities = 21/101 (20%), Positives = 48/101 (47%), Gaps = 6/101 (5%) Query: 35 RNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGY 94 R++ +QL + + E +LL+G GK+ I +++ L G F + E+ ++ + Y Sbjct: 15 RSKEIDKQLKKEKKKEKKIIKLLLLGAGESGKSTIVKQMKILHGDGFSEEELLEYRPVIY 74 Query: 95 VGRNVEQIIRDLVD----VAINIVRESRRDEVREQASINAE 131 N+ Q ++ L+ + IN+ R ++ ++ + Sbjct: 75 --SNIIQSLKALLRAMETLGINLDDPERENDAQKLTLLADA 113 >gnl|CDD|31748 COG1560, HtrB, Lauroyl/myristoyl acyltransferase [Cell envelope biogenesis, outer membrane]. Length = 308 Score = 28.7 bits (64), Expect = 3.5 Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 10/56 (17%) Query: 195 LFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIVFLD 250 L +++ RK R ++ C+PE E ++++ + + G L+ Sbjct: 46 LAGRLLKRRRKI-ARRNLALCFPEKSEAEREKIVK---------ESFASMGRALLE 91 >gnl|CDD|35958 KOG0739, KOG0739, KOG0739, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 439 Score = 28.4 bits (63), Expect = 3.7 Identities = 33/118 (27%), Positives = 52/118 (44%), Gaps = 18/118 (15%) Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHILFIASGAFH 305 I+F+DE D + S N SR ++ + L ++G + D +L + + Sbjct: 228 IIFIDEIDSLCGSRSENESEASRR-IKTEFLVQMQGVGN-------DNDGVLVLGA---- 275 Query: 306 VSRPADLLPEIQGRFPVRVHLKSLNKSD----FRLILTDTESNLILQ-YKEL-MKTEG 357 + P L I+ RF R+++ F+L L DT L Q +KEL KTEG Sbjct: 276 TNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEG 333 Score = 28.0 bits (62), Expect = 4.6 Identities = 16/57 (28%), Positives = 34/57 (59%), Gaps = 2/57 (3%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 + ILL GP G GK+ +++ +A A + F V + ++G + E+++++L ++A Sbjct: 167 RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS-KWMGES-EKLVKNLFEMA 221 >gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members. Length = 268 Score = 28.7 bits (65), Expect = 3.7 Identities = 12/25 (48%), Positives = 15/25 (60%) Query: 55 NILLVGPTGVGKTAISRRLARLAGA 79 NI LVG +G GKT ++ L GA Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGA 25 >gnl|CDD|32539 COG2403, COG2403, Predicted GTPase [General function prediction only]. Length = 449 Score = 28.4 bits (63), Expect = 3.9 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 3/89 (3%) Query: 62 TGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDE 121 TGVGK+A+SR +ARL +V V + I Y G +E + L + ++ R + DE Sbjct: 136 TGVGKSAVSRYVARLLRERGYRVCVVRHPMI-YRGDRIEITVERLAKLE-DLDRHAATDE 193 Query: 122 VREQASINAEERILDALVGKTATSNTREV 150 RE + L G + +E Sbjct: 194 ERE-EYESYIPTGGGVLAGVDYGTVLKEG 221 >gnl|CDD|33404 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]. Length = 550 Score = 28.4 bits (63), Expect = 4.0 Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 3/33 (9%) Query: 55 NILLVGPTGVGKTAISRRLARL---AGAPFIKV 84 +L+ G TG GK ++R + +L PF+K+ Sbjct: 248 TVLIRGETGTGKELVARAIHQLSPRRDKPFVKL 280 >gnl|CDD|133261 cd01852, AIG1, AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins). Length = 196 Score = 28.3 bits (64), Expect = 4.1 Identities = 8/15 (53%), Positives = 11/15 (73%) Query: 54 KNILLVGPTGVGKTA 68 ++LVG TG GK+A Sbjct: 1 LRLVLVGKTGAGKSA 15 >gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Length = 429 Score = 28.2 bits (63), Expect = 4.5 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 7/68 (10%) Query: 25 DAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG---KTAISRRLARLAGAPF 81 + ++A + + RR+ L +L++ P + G +T + + GAP+ Sbjct: 2 NQEKAAKLYAQLAGRREDLENELQEVFPPWYV----SDGFVPKKRTTNNSVRGYVKGAPY 57 Query: 82 IKVEVTKF 89 K+++ F Sbjct: 58 TKIKLVTF 65 >gnl|CDD|35279 KOG0056, KOG0056, KOG0056, Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]. Length = 790 Score = 28.1 bits (62), Expect = 4.6 Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%) Query: 46 DLRDELMP-KNILLVGPTGVGKTAISRRLARL 76 D+ + P K + LVGP+G GK+ I R L R Sbjct: 556 DISFTVQPGKTVALVGPSGAGKSTIMRLLFRF 587 >gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional. Length = 489 Score = 28.1 bits (63), Expect = 4.7 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 2/58 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 P+ +LLVG G GK+ ++ +A P ++++V K G VG + E +R ++ +A Sbjct: 259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFG-GIVGES-ESRMRQMIRIA 314 >gnl|CDD|33684 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense mechanisms]. Length = 205 Score = 28.1 bits (62), Expect = 4.7 Identities = 11/36 (30%), Positives = 20/36 (55%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91 +LL G + GK++I+ LA P++ + + F E Sbjct: 26 VLLNGGSSAGKSSIALAFQDLAAEPWMHIGIDLFWE 61 >gnl|CDD|35575 KOG0354, KOG0354, KOG0354, DEAD-box like helicase [General function prediction only]. Length = 746 Score = 28.0 bits (62), Expect = 4.8 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 8/62 (12%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRD---EL----MPKNILLVGPTGVGKTAISRR 72 I A ++ + RW +LR+ EL + KN ++ PTG GKT I+ Sbjct: 37 IDQNNSASHSLDESAAQRWIYPT-NLELRNYQEELVQPALGKNTIIALPTGSGKTFIAAV 95 Query: 73 LA 74 + Sbjct: 96 IM 97 >gnl|CDD|31320 COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]. Length = 539 Score = 28.2 bits (63), Expect = 4.9 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%) Query: 50 ELMPKNIL-LVGPTGVGKTAISRRLARL 76 +L L LVG +G GK+ ++R LA L Sbjct: 313 DLREGETLGLVGESGSGKSTLARILAGL 340 >gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction only]. Length = 296 Score = 28.0 bits (62), Expect = 5.3 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 4/61 (6%) Query: 32 IALRNRWRRQQLPADLRD----ELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVT 87 + +++ LR E P N+LL+G TG GK+++ L + KV V Sbjct: 14 LLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVG 73 Query: 88 K 88 Sbjct: 74 T 74 >gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and metabolism]. Length = 208 Score = 27.9 bits (62), Expect = 5.3 Identities = 12/54 (22%), Positives = 23/54 (42%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRD 105 I++ G G GKT + L IKV +T+ +G + +++ + Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGTPIGEKIRELLLN 55 >gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).. Length = 166 Score = 27.8 bits (62), Expect = 5.5 Identities = 10/23 (43%), Positives = 16/23 (69%) Query: 54 KNILLVGPTGVGKTAISRRLARL 76 +L+ GP+G GK+++ R LA L Sbjct: 28 DRLLITGPSGTGKSSLFRALAGL 50 >gnl|CDD|153328 cd07644, I-BAR_IMD_BAIAP2L2, Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. This group is composed of uncharacterized proteins known as BAIAP2L2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2). They contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The related proteins, BAIAP2L1 and IRSp53, function as regulators of membrane dynamics and the actin cytoskeleton. The IMD domain binds and bundles actin filaments, binds membranes and produces membrane protrusions, and interacts with the small GTPase Rac. Length = 215 Score = 28.0 bits (62), Expect = 5.5 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%) Query: 369 ALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDAEYV 419 AL++ A S + IG + LQ++ + L +I S+ Q + + D E V Sbjct: 38 ALSEAAEVYFSAIAKIGEQALQSLTSQSLGEILIQMSETQ-RKLSADLEVV 87 >gnl|CDD|35283 KOG0060, KOG0060, KOG0060, Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism, General function prediction only]. Length = 659 Score = 28.0 bits (62), Expect = 5.8 Identities = 11/23 (47%), Positives = 17/23 (73%) Query: 54 KNILLVGPTGVGKTAISRRLARL 76 +N+L+ GP+G GKT++ R L L Sbjct: 462 QNLLITGPSGCGKTSLLRVLGGL 484 >gnl|CDD|30481 COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]. Length = 223 Score = 27.9 bits (62), Expect = 6.1 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 1/38 (2%) Query: 52 MPKNILLVGP-TGVGKTAISRRLARLAGAPFIKVEVTK 88 M K + G TGVGKT +S LA+ V K Sbjct: 1 MMKRFFVTGTDTGVGKTVVSAALAQALKQQGYSVAGYK 38 >gnl|CDD|31674 COG1485, COG1485, Predicted ATPase [General function prediction only]. Length = 367 Score = 27.9 bits (62), Expect = 6.4 Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 9/58 (15%) Query: 10 REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67 + LDR + + A R+ AL + R P + + L G G GKT Sbjct: 31 PAAAAALDR-LYDELVAPRSARKALGWLFGRDHGP--------VRGLYLWGGVGRGKT 79 >gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160 Score = 27.9 bits (63), Expect = 6.5 Identities = 7/19 (36%), Positives = 14/19 (73%) Query: 55 NILLVGPTGVGKTAISRRL 73 ++++G GVGK+AI+ + Sbjct: 1 KVVVLGAGGVGKSAITIQF 19 >gnl|CDD|31308 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]. Length = 542 Score = 27.5 bits (61), Expect = 6.8 Identities = 11/17 (64%), Positives = 14/17 (82%) Query: 54 KNILLVGPTGVGKTAIS 70 KN L+V PTG+GKT I+ Sbjct: 30 KNTLVVLPTGLGKTFIA 46 >gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]. Length = 515 Score = 27.7 bits (61), Expect = 7.1 Identities = 25/78 (32%), Positives = 30/78 (38%), Gaps = 21/78 (26%) Query: 56 ILLVGPTGVGKTAISRRLAR-------LAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108 L GP GVGKT I+R LA+ P K K G L+D Sbjct: 41 YLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGS-----------LID 89 Query: 109 VAINIVRESRR--DEVRE 124 V I I S D++RE Sbjct: 90 V-IEIDAASNTGVDDIRE 106 >gnl|CDD|29278 cd00227, CPT, Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.. Length = 175 Score = 27.6 bits (61), Expect = 7.2 Identities = 12/36 (33%), Positives = 20/36 (55%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91 I+L G + GK++I+R L + P++ V F E Sbjct: 5 IILNGGSSAGKSSIARALQSVLAEPWLHFGVDSFIE 40 >gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only]. Length = 398 Score = 27.6 bits (61), Expect = 7.5 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 6/78 (7%) Query: 7 FSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGK 66 S + + + + +D + + W + A +M +VGP GK Sbjct: 33 LSVARVRTTYHQLVEVPEDRSEP-LEEIADTWESKSESAGKVGVVM-----VVGPVDSGK 86 Query: 67 TAISRRLARLAGAPFIKV 84 + ++ LA A KV Sbjct: 87 STLTTYLANKLLARGRKV 104 >gnl|CDD|33622 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]. Length = 560 Score = 27.6 bits (61), Expect = 7.8 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%) Query: 52 MPKNILLVGPTGVGKTAISRRLARL---AGAPFIKV 84 +L++G +G GK +R + L A PFI + Sbjct: 267 TDSTVLILGESGTGKELFARAIHNLSPRANGPFIAI 302 >gnl|CDD|31434 COG1241, MCM2, Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]. Length = 682 Score = 27.6 bits (61), Expect = 7.9 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 16/76 (21%) Query: 11 EIVSELDRYII----GQQDAKRAVAIAL-----RNRWRRQQLPADLRDELMPKNILLVGP 61 +I L + I G +D K+A+ + L +N ++ D+ +ILLVG Sbjct: 275 DIYDILIKSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDI-------HILLVGD 327 Query: 62 TGVGKTAISRRLARLA 77 G K+ + + +A+LA Sbjct: 328 PGTAKSQLLKYVAKLA 343 >gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family. Length = 327 Score = 27.5 bits (62), Expect = 7.9 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 12/63 (19%) Query: 20 IIGQQDAKRAVAIAL-----RNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74 I G +D K+A+ + L +N +L D+ N+LLVG G K+ + + +A Sbjct: 26 IYGHEDVKKAILLQLFGGVKKNLPDGTRLRGDI-------NVLLVGDPGTAKSQLLKYVA 78 Query: 75 RLA 77 +LA Sbjct: 79 KLA 81 >gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction only]. Length = 849 Score = 27.3 bits (60), Expect = 8.2 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 11/87 (12%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVE-----QIIRDLVDV- 109 +L+ G +G+GK+A+ + + KF + RN+ Q RDL+ Sbjct: 27 VLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQF---ERNIPLSPLVQAFRDLMGQL 83 Query: 110 --AINIVRESRRDEVREQASINAEERI 134 + S R + N + I Sbjct: 84 LSESDTRILSWRARLLAALGENGQVII 110 >gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 157 Score = 27.2 bits (60), Expect = 8.3 Identities = 10/31 (32%), Positives = 17/31 (54%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 + LVGP G GK+ + R +A L ++ + Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILI 58 >gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]. Length = 254 Score = 27.3 bits (60), Expect = 8.5 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 4/28 (14%) Query: 52 MPKNILLVGPTGVGKT----AISRRLAR 75 +N++L+GP GVGKT AI L + Sbjct: 104 RGENLVLLGPPGVGKTHLAIAIGNELLK 131 >gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.. Length = 193 Score = 27.1 bits (60), Expect = 8.6 Identities = 8/27 (29%), Positives = 15/27 (55%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82 I++ G G GK+ +++ LA G + Sbjct: 2 IVVEGNIGAGKSTLAKELAEHLGYEVV 28 >gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 179 Score = 27.1 bits (60), Expect = 8.7 Identities = 10/27 (37%), Positives = 14/27 (51%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82 I + G G GKT ++R LA G + Sbjct: 3 ITISGLPGSGKTTVARELAEHLGLKLV 29 >gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 27.2 bits (60), Expect = 9.3 Identities = 26/119 (21%), Positives = 43/119 (36%), Gaps = 23/119 (19%) Query: 56 ILLVGPTGVGKTAISRRLARLA----GAPFIKVEVTKFTE--------IGYVGRNVE-QI 102 +LL+GP G GK+ + + L L G + T + +G V +N + Q+ Sbjct: 33 VLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLELRQKVGLVFQNPDDQL 92 Query: 103 IRDLV--DVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGE 159 V +VA + E EER+ +AL + L G+ Sbjct: 93 FGPTVEDEVAFGLENLGLPRE-------EIEERVAEALE-LVGLEELLDRPPFNLSGGQ 143 >gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing and modification]. Length = 674 Score = 27.2 bits (60), Expect = 9.6 Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 6/34 (17%) Query: 40 RQQLP-ADLRDELMP-----KNILLVGPTGVGKT 67 R+ LP RD+++ + ++++G TG GK+ Sbjct: 47 RESLPIYKYRDQILYAVEDNQVLIVIGETGSGKS 80 >gnl|CDD|31564 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 398 Score = 26.9 bits (59), Expect = 9.9 Identities = 12/33 (36%), Positives = 18/33 (54%) Query: 50 ELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 +L P IL++GP VGKT + + L + I Sbjct: 34 DLRPFIILILGPRQVGKTTLLKLLIKGLLEEII 66 >gnl|CDD|30199 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.. Length = 273 Score = 27.1 bits (60), Expect = 9.9 Identities = 10/27 (37%), Positives = 15/27 (55%) Query: 58 LVGPTGVGKTAISRRLARLAGAPFIKV 84 + G +G GK+ RRL L G+ + V Sbjct: 4 VAGDSGCGKSTFLRRLTSLFGSDLVTV 30 >gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55 [Replication, recombination and repair]. Length = 326 Score = 26.9 bits (59), Expect = 10.0 Identities = 13/28 (46%), Positives = 14/28 (50%) Query: 57 LLVGPTGVGKTAISRRLARLAGAPFIKV 84 LVGP G GKT + LA G KV Sbjct: 115 ELVGPPGSGKTQLCHTLAVTCGGGEGKV 142 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 0.319 0.137 0.376 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,092,510 Number of extensions: 276548 Number of successful extensions: 1304 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1286 Number of HSP's successfully gapped: 222 Length of query: 437 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 340 Effective length of database: 4,167,664 Effective search space: 1417005760 Effective search space used: 1417005760 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: 59 (26.5 bits)