RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 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|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional. Length = 443 Score = 708 bits (1830), Expect = 0.0 Identities = 252/443 (56%), Positives = 331/443 (74%), Gaps = 13/443 (2%) Query: 6 NFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVG 65 +PREIVSELD+YIIGQ DAKRAVAIALRNRWRR QLP +LRDE+ PKNIL++GPTGVG Sbjct: 3 ELTPREIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVG 62 Query: 66 KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQ 125 KT I+RRLA+LA APFIKVE TKFTE+GYVGR+VE IIRDLV++A+ +VRE +R++VRE+ Sbjct: 63 KTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVREK 122 Query: 126 ASINAEERILDALVGK-----------TATSNTREVFRKKLRDGEISDKEIDIEVADTSS 174 A AEERILDAL+ S TR+ FRKKLR+GE+ DKEI+IEVA+ + Sbjct: 123 AEEAAEERILDALLPPAKNNWGEEEEKEEISATRQKFRKKLREGELDDKEIEIEVAEAAP 182 Query: 175 DISNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVH 234 + PG + I L ++F + +KKK ++ V++ L+ +E+ +LIDM+ + Sbjct: 183 MMEIMGPPGMEEMTI-QLQDMFGNLGP-KKKKKRKLKVKEARKILIEEEAAKLIDMEEIK 240 Query: 235 RDSIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTD 294 +++I+ VE GIVF+DE DKI AR +G VSREGVQRDLLPLVEGS+VSTKYG + TD Sbjct: 241 QEAIERVEQNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTD 300 Query: 295 HILFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMK 354 HILFIASGAFHVS+P+DL+PE+QGRFP+RV L +L + DF ILT+ +++LI QY+ L+ Sbjct: 301 HILFIASGAFHVSKPSDLIPELQGRFPIRVELDALTEEDFVRILTEPKASLIKQYQALLA 360 Query: 355 TEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVI 414 TEG+ L+FT+D+I +A++A +N +IGARRL TVME++LEDISF A D+ +TV I Sbjct: 361 TEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDMSGETVTI 420 Query: 415 DAEYVRLHIGDFPSETDMYHFIL 437 DA YV +GD + D+ +IL Sbjct: 421 DAAYVDEKLGDLVKDEDLSRYIL 443 >gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit. This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment. Length = 441 Score = 512 bits (1319), Expect = e-146 Identities = 224/441 (50%), Positives = 318/441 (72%), Gaps = 12/441 (2%) Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKT 67 +PREIV+ELD+YIIGQ +AK++VAIALRNR+RR QL +L+DE+ PKNIL++GPTGVGKT Sbjct: 2 TPREIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKT 61 Query: 68 AISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQAS 127 I+RRLA+LA APFIKVE TKFTE+GYVGR+VE ++RDL D A+ +V+E ++VR++A Sbjct: 62 EIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAVKLVKEEAIEKVRDRAE 121 Query: 128 INAEERILDALV-----------GKTATSNTREVFRKKLRDGEISDKEIDIEVADTSSDI 176 AEERI+D L+ + + RE FRKKLR+GE+ DKEI+I+V+ Sbjct: 122 ELAEERIVDVLLPPAKNQWGQTEQQQEPESAREAFRKKLREGELDDKEIEIDVSAKMPSG 181 Query: 177 SNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRD 236 P G + L LF + G +KKK ++ ++ L+ +E+ +L+D + + ++ Sbjct: 182 IEIMAPPGMEEMTMQLQSLFQNLGGQ-KKKKRKLKIKDAKKALIAEEAAKLVDPEEIKQE 240 Query: 237 SIQMVENYGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHI 296 +I VE GI+F+DE DKI + +G VSREGVQRDLLP+VEGS+V+TKYG + TDHI Sbjct: 241 AIDAVEQSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHI 300 Query: 297 LFIASGAFHVSRPADLLPEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTE 356 LFIA+GAF +++P+DL+PE+QGRFP+RV L++L DF ILT+ +++LI QYK LMKTE Sbjct: 301 LFIAAGAFQLAKPSDLIPELQGRFPIRVELQALTTDDFERILTEPKNSLIKQYKALMKTE 360 Query: 357 GIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQEKTVVIDA 416 G+ ++F++++I +A++A N+N +IGARRL TV+ER+LEDISF A DL + + IDA Sbjct: 361 GVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLEDISFEAPDLSGQNITIDA 420 Query: 417 EYVRLHIGDFPSETDMYHFIL 437 +YV +G ++ D+ FIL Sbjct: 421 DYVSKKLGALVADEDLSRFIL 441 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 121 bits (305), Expect = 4e-28 Identities = 70/232 (30%), Positives = 112/232 (48%), Gaps = 63/232 (27%) Query: 245 GIVFLDEFDKIVARDSGNGIG---VSREGVQRDLLPLVEGSSVS-----------TKYGS 290 GIV++DE DKI AR S N VS EGVQ+ LL ++EG+ S ++ Sbjct: 175 GIVYIDEIDKI-ARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQ 233 Query: 291 INTDHILFIASGAF------------------------------------HVSRPADLL- 313 ++T +ILFI GAF V P DL+ Sbjct: 234 VDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQV-EPEDLIK 292 Query: 314 ----PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDA 369 PE GR PV L+ L++ ILT+ ++ L+ QY++L + +G+ L+FT+++++A Sbjct: 293 FGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEA 352 Query: 370 LADVAVNLNSTVGDIGARRLQTVMERVLEDISFSASDLQE-KTVVIDAEYVR 420 +A A+ + GAR L++++E +L D+ F ++ + VVI E V Sbjct: 353 IAKKAIERKT-----GARGLRSILEEILLDVMFELPSREDVEKVVITKEVVE 399 Score = 105 bits (264), Expect = 3e-23 Identities = 45/105 (42%), Positives = 68/105 (64%), Gaps = 2/105 (1%) Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRD--ELMPKNILLVGPTGVG 65 +P+EI + LD+Y+IGQ+ AK+ +++A+ N ++R + D EL NILL+GPTG G Sbjct: 61 TPKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSG 120 Query: 66 KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 KT +++ LAR+ PF + T TE GYVG +VE I+ L+ A Sbjct: 121 KTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAA 165 >gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. Length = 413 Score = 101 bits (253), Expect = 4e-22 Identities = 71/229 (31%), Positives = 107/229 (46%), Gaps = 61/229 (26%) Query: 245 GIVFLDEFDKIVARDSGNGI--GVSREGVQRDLLPLVEGS--SVSTKYG---------SI 291 GI+++DE DKI + I VS EGVQ+ LL ++EG+ +V + G I Sbjct: 183 GIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQI 242 Query: 292 NTDHILFIASGAF---------------------------------HVSRPADLL----- 313 +T +ILFI GAF P DL+ Sbjct: 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLI 302 Query: 314 PEIQGRFPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDALADV 373 PE GR PV L+ L++ ILT ++ L+ QY+ L K + + LDF E+++ A+A Sbjct: 303 PEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKK 362 Query: 374 AVNLNSTVGDIGARRLQTVMERVLEDISF---SASDLQEKTVVIDAEYV 419 A+ + GAR L++++E +L D+ F S DL++ VVI E V Sbjct: 363 ALERKT-----GARGLRSIVEGLLLDVMFDLPSLEDLEK--VVITKETV 404 Score = 90.6 bits (225), Expect = 7e-19 Identities = 45/107 (42%), Positives = 67/107 (62%), Gaps = 4/107 (3%) Query: 8 SPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLP----ADLRDELMPKNILLVGPTG 63 +P+EI + LD Y+IGQ+ AK+ +++A+ N ++R +D EL NILL+GPTG Sbjct: 67 TPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTG 126 Query: 64 VGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 GKT +++ LAR+ PF + T TE GYVG +VE I+ L+ A Sbjct: 127 SGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAA 173 >gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168 Score = 83.0 bits (206), Expect = 2e-16 Identities = 40/187 (21%), Positives = 65/187 (34%), Gaps = 60/187 (32%) Query: 176 ISNFDIPGGASVGILNLSELFSKVMGSGRKKKIR--MSVQKCYPELMRDESDRLIDMDTV 233 I +F G VG L++ ++++ + IR MS E M + + Sbjct: 3 IGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMS------EYM---EEHSVSRLIG 53 Query: 234 HRDSIQMVEN------------YGIVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLVEG 281 E Y IV +DE +K GVQ DLL ++EG Sbjct: 54 APPGYVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHP------------GVQNDLLQILEG 101 Query: 282 SSVSTKYGS-INTDHILFIASGAFHVSRPAD------------------------LLPEI 316 +++ K G ++ + LFI +G F + +D +PE Sbjct: 102 GTLTDKQGRKVDFRNTLFIMTGNFGSEKISDASRLGKSPDYELLKELVMDLLKKGFIPEF 161 Query: 317 QGRFPVR 323 GR P+ Sbjct: 162 LGRLPII 168 Score = 40.3 bits (95), Expect = 0.001 Identities = 14/40 (35%), Positives = 26/40 (65%), Gaps = 3/40 (7%) Query: 55 NILLVGPTGVGKTAISRRLARLAG---APFIKVEVTKFTE 91 + L +GPTGVGKT +++ LA L I+++++++ E Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME 44 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 45.8 bits (109), Expect = 2e-05 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 18/94 (19%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPK-NILLVGPTGVGKTAISRRL 73 L I GQ +A ++ +++ R R A L + P + L GPTGVGKT ++++L Sbjct: 451 NLKAKIFGQDEAIDSLVSSIK-RSR-----AGLGNPNKPVGSFLFTGPTGVGKTELAKQL 504 Query: 74 ARLAGAPFIKVEVTKFTE-----------IGYVG 96 A G + +++++ E GYVG Sbjct: 505 AEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVG 538 Score = 30.8 bits (70), Expect = 0.77 Identities = 14/22 (63%), Positives = 15/22 (68%) Query: 55 NILLVGPTGVGKTAISRRLARL 76 N LLVG GVGKTAI+ LA Sbjct: 205 NPLLVGEPGVGKTAIAEGLALR 226 >gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. Length = 495 Score = 42.3 bits (100), Expect = 2e-04 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 7/77 (9%) Query: 34 LRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIG 93 L+N + +L A + PK +LLVGP G GKT +++ +A AG PF + + F E+ Sbjct: 74 LKNPSKFTKLGAKI-----PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM- 127 Query: 94 YVGRNVEQIIRDLVDVA 110 +VG + +RDL + A Sbjct: 128 FVGVGASR-VRDLFEQA 143 >gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional. Length = 184 Score = 42.2 bits (100), Expect = 3e-04 Identities = 15/38 (39%), Positives = 22/38 (57%) Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 R L + ++LVG G GK+ + RRLA + G PF+ Sbjct: 2 ERARAALGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL 39 >gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed. Length = 175 Score = 42.1 bits (100), Expect = 3e-04 Identities = 15/32 (46%), Positives = 19/32 (59%) Query: 51 LMPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 L NI+L+G G GK+ I R LA+ G FI Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFI 33 >gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed. Length = 644 Score = 40.8 bits (95), Expect = 6e-04 Identities = 31/94 (32%), Positives = 49/94 (52%), Gaps = 10/94 (10%) Query: 20 IIGQQDAKRAVAIA---LRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARL 76 + G +AK VA LR R Q+L + PK +L+VGP G GKT +++ +A Sbjct: 154 VAGCDEAKEEVAELVEYLREPSRFQKLGGKI-----PKGVLMVGPPGTGKTLLAKAIAGE 208 Query: 77 AGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVA 110 A PF + + F E+ +VG + +RD+ + A Sbjct: 209 AKVPFFTISGSDFVEM-FVGVGASR-VRDMFEQA 240 >gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional. Length = 389 Score = 40.6 bits (96), Expect = 7e-04 Identities = 37/107 (34%), Positives = 54/107 (50%), Gaps = 25/107 (23%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE----VTKFTEIGYVGRNVEQIIRDLVD 108 PK +LL GP G GKT +++ +A A FI+V V KF IG R ++R+L + Sbjct: 165 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKF--IGEGAR----LVRELFE 218 Query: 109 VAINIVRESRRDEVREQASINAEERILDALVGK---TATSNTREVFR 152 +A RE + + I +E +DA+ K + TS REV R Sbjct: 219 LA----RE------KAPSIIFIDE--IDAIAAKRTDSGTSGDREVQR 253 Score = 29.0 bits (66), Expect = 2.7 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%) Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPL 278 I+F+DE D I A+ + +G RE VQR L+ L Sbjct: 227 IIFIDEIDAIAAKRTDSGTSGDRE-VQRTLMQL 258 >gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional. Length = 857 Score = 40.2 bits (94), Expect = 0.001 Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 10/89 (11%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73 EL +IGQ +A AV+ A+R R R A L D P + L +GPTGVGKT + + L Sbjct: 565 ELHHRVIGQNEAVEAVSNAIR-RSR-----AGLSDPNRPIGSFLFLGPTGVGKTELCKAL 618 Query: 74 ARL---AGAPFIKVEVTKFTEIGYVGRNV 99 A + +++++++F E V R V Sbjct: 619 ANFMFDSDDAMVRIDMSEFMEKHSVSRLV 647 >gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. Length = 852 Score = 40.3 bits (95), Expect = 0.001 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 7/61 (11%) Query: 15 ELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMP-KNILLVGPTGVGKTAISRRL 73 L ++GQ +A AV+ A+R R R A L D P + L +GPTGVGKT +++ L Sbjct: 562 VLHERVVGQDEAVEAVSDAIR-RSR-----AGLSDPNRPIGSFLFLGPTGVGKTELAKAL 615 Query: 74 A 74 A Sbjct: 616 A 616 Score = 27.2 bits (61), Expect = 9.2 Identities = 12/21 (57%), Positives = 15/21 (71%) Query: 55 NILLVGPTGVGKTAISRRLAR 75 N +L+G GVGKTAI LA+ Sbjct: 196 NPVLIGEPGVGKTAIVEGLAQ 216 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 39.5 bits (92), Expect = 0.002 Identities = 38/138 (27%), Positives = 64/138 (46%), Gaps = 21/138 (15%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVE----VTKFTEIGYVGRNVEQIIRDLVD 108 PK +LL GP G GKT +++ +A AGA FI + ++K+ G + +I ++ + Sbjct: 212 PKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKY--YGESEERLREIFKEAEE 269 Query: 109 VAINIVRESRRDEV---REQASINAEERI-------LDALVGK-----TATSNTREVFRK 153 A +I+ D + RE+ + E+R+ +D L G+ +N + Sbjct: 270 NAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329 Query: 154 KLRDGEISDKEIDIEVAD 171 LR D+EI I V D Sbjct: 330 ALRRPGRFDREIVIRVPD 347 Score = 34.9 bits (80), Expect = 0.044 Identities = 16/32 (50%), Positives = 22/32 (68%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKV 84 PK +LL GP G GKT +++ +A +GA FI V Sbjct: 487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAV 518 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 39.2 bits (92), Expect = 0.002 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 6/69 (8%) Query: 10 REIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAI 69 RE++ +L +DA R + AL + ++ ++ I LVGPTGVGKT Sbjct: 154 RELLEKLPERA-DAEDAWRWLREALEKMLPVKPEEDEILEQ--GGVIALVGPTGVGKTTT 210 Query: 70 SRRLARLAG 78 LA+LA Sbjct: 211 ---LAKLAA 216 >gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed. Length = 307 Score = 39.0 bits (92), Expect = 0.003 Identities = 13/24 (54%), Positives = 18/24 (75%) Query: 52 MPKNILLVGPTGVGKTAISRRLAR 75 PK I++VGPT GKTA++ LA+ Sbjct: 3 KPKVIVIVGPTASGKTALAIELAK 26 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 38.5 bits (89), Expect = 0.003 Identities = 16/34 (47%), Positives = 20/34 (58%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 + IL+VGP G GKT ++R LAR G P V Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIY 35 >gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 139 Score = 38.4 bits (90), Expect = 0.003 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 4/68 (5%) Query: 55 NILLVGPTGVGKTAISRRLA-RLAGAPFIKVEVTKFTEIGYV--GRNVEQIIRDLVD-VA 110 +LLVGP G GK+ ++ RLA L+ P V++T+ T + RN+ VD Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60 Query: 111 INIVRESR 118 + RE Sbjct: 61 VRAAREGE 68 >gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain. Length = 499 Score = 37.5 bits (87), Expect = 0.007 Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 16/54 (29%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73 I GQQ AKRA+ IA N+LL GP G GKT ++ RL Sbjct: 194 IKGQQHAKRALEIAAAGG----------------HNLLLFGPPGSGKTMLASRL 231 >gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. Length = 775 Score = 37.3 bits (87), Expect = 0.009 Identities = 13/40 (32%), Positives = 24/40 (60%) Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 LR ++ + LVGP GVGKT++ + +A+ F++ + Sbjct: 341 LRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSL 380 >gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system. Length = 852 Score = 36.8 bits (86), Expect = 0.010 Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 9/54 (16%) Query: 16 LDRYIIGQQDAKRAVAIALRN-RWRRQQLPADLRDELMPKNI-LLVGPTGVGKT 67 L +IGQ A A+A +R R A L D P + LLVGP+GVGKT Sbjct: 564 LAERVIGQDHALEAIAERIRTAR-------AGLEDPRKPLGVFLLVGPSGVGKT 610 Score = 27.6 bits (62), Expect = 7.3 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 55 NILLVGPTGVGKTAISRRLAR 75 N +L G GVGKTA+ LA Sbjct: 210 NPILTGEAGVGKTAVVEGLAL 230 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 36.8 bits (86), Expect = 0.011 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 10/71 (14%) Query: 10 REIVSEL-DRYIIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNIL-LVGPTGVGKT 67 +++ L + ++ A R + L N +P + D L ++ LVGPTGVGKT Sbjct: 181 EKLLKLLLEHMPPRERTAWRYLLELLAN-----MIPVRVEDILKQGGVVALVGPTGVGKT 235 Query: 68 AISRRLARLAG 78 LA+LA Sbjct: 236 TT---LAKLAA 243 >gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal. Length = 364 Score = 36.3 bits (84), Expect = 0.018 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE--IGYVGRNVEQIIR 104 PK +LL GP G GKT +++ +A A FI+V ++ IG R V +I Sbjct: 156 PKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFE 209 Score = 28.2 bits (63), Expect = 4.3 Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 1/34 (2%) Query: 246 IVFLDEFDKIVARDSGNGIGVSREGVQRDLLPLV 279 I+F+DE D I A+ + +G RE VQR L+ L+ Sbjct: 218 IIFIDEIDAIAAKRTDSGTSGDRE-VQRTLMQLL 250 >gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional. Length = 171 Score = 36.2 bits (84), Expect = 0.018 Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKV--EVTKFTE 91 KNI+L+G G GKT + +R+A FI E+ K T Sbjct: 2 KNIVLIGFMGTGKTTVGKRVATTLSFGFIDTDKEIEKMTG 41 >gnl|CDD|163076 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. Length = 365 Score = 36.1 bits (84), Expect = 0.019 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 13/75 (17%) Query: 53 PKNILLVGPTGVGKTAISR----RLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108 P N+ + G TG GKTA+++ L A + + V N QI+ L Sbjct: 40 PSNVFIYGKTGTGKTAVTKYVMKELEEAAE--------DRDVRVVTVYVNC-QILDTLYQ 90 Query: 109 VAINIVRESRRDEVR 123 V + + + R Sbjct: 91 VLVELANQLRGSGEE 105 >gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional. Length = 459 Score = 35.8 bits (82), Expect = 0.020 Identities = 17/30 (56%), Positives = 22/30 (73%) Query: 47 LRDELMPKNILLVGPTGVGKTAISRRLARL 76 L+ + KNI+L GP GVGKT ++RRLA L Sbjct: 188 LKRLTIKKNIILQGPPGVGKTFVARRLAYL 217 >gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional. Length = 398 Score = 35.5 bits (82), Expect = 0.024 Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 9/87 (10%) Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAP 80 I +Q+ + AV + L +Q+ D P+ +LL GP G GKT +++ +A A Sbjct: 152 IQKQEIREAVELPLTCPELYEQIGID-----PPRGVLLYGPPGTGKTMLAKAVAHHTTAT 206 Query: 81 FIKVEVTKFTEIGYVG---RNVEQIIR 104 FI+V ++F + Y+G R V + R Sbjct: 207 FIRVVGSEFVQ-KYLGEGPRMVRDVFR 232 >gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional. Length = 758 Score = 34.8 bits (80), Expect = 0.040 Identities = 14/41 (34%), Positives = 26/41 (63%) Query: 57 LLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGR 97 L GPTGVGKT ++ +L++ G ++ +++++ E V R Sbjct: 492 LFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSR 532 Score = 30.6 bits (69), Expect = 0.84 Identities = 14/20 (70%), Positives = 16/20 (80%) Query: 55 NILLVGPTGVGKTAISRRLA 74 N LLVG +GVGKTAI+ LA Sbjct: 209 NPLLVGESGVGKTAIAEGLA 228 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 33.1 bits (77), Expect = 0.13 Identities = 12/30 (40%), Positives = 19/30 (63%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV 84 +++L GP G GKT ++R +A APF + Sbjct: 38 SMILWGPPGTGKTTLARIIAGATDAPFEAL 67 >gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional. Length = 169 Score = 33.2 bits (76), Expect = 0.15 Identities = 14/29 (48%), Positives = 16/29 (55%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFI 82 I LVG G GKT + + LAR G FI Sbjct: 2 ARIFLVGYMGAGKTTLGKALARELGLSFI 30 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 32.8 bits (75), Expect = 0.17 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 3/36 (8%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT 90 NI+L+GP+GVGKT ++ L A IK +FT Sbjct: 104 NIVLLGPSGVGKTHLAIALGYEAVRAGIK---VRFT 136 >gnl|CDD|179921 PRK05057, aroK, shikimate kinase I; Reviewed. Length = 172 Score = 32.8 bits (75), Expect = 0.20 Identities = 13/22 (59%), Positives = 17/22 (77%) Query: 54 KNILLVGPTGVGKTAISRRLAR 75 +NI LVGP G GK+ I R+LA+ Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQ 26 >gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. Length = 305 Score = 32.7 bits (75), Expect = 0.21 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 9/54 (16%) Query: 21 IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74 IGQ+ K + + + A +R E ++LL GP G+GKT ++ +A Sbjct: 7 IGQEKVKEQLQLFIE--------AAKMRQE-ALDHLLLYGPPGLGKTTLAHIIA 51 >gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed. Length = 171 Score = 32.2 bits (74), Expect = 0.27 Identities = 12/31 (38%), Positives = 17/31 (54%) Query: 52 MPKNILLVGPTGVGKTAISRRLARLAGAPFI 82 M + + LVG G GKT + LA+ G F+ Sbjct: 1 MTQPLFLVGARGCGKTTVGMALAQALGYRFV 31 >gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. Length = 615 Score = 32.1 bits (73), Expect = 0.31 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 6/44 (13%) Query: 53 PKNILLVGPTGVGKTAISR----RLARLAGAPFIKVEVTKFTEI 92 P++I+L GP GVGKT +R +L PF E F E+ Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPF--AEDAPFVEV 216 >gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 420 Score = 31.8 bits (72), Expect = 0.33 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 13/78 (16%) Query: 3 LTFNFSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADLR----DELMPKNIL- 57 L+ FSP L R+++ + A R +L+ L +LR DE++ + + Sbjct: 142 LSAGFSP-----LLSRHLLEKLPADRDFEQSLK--KTISLLTLNLRTIGGDEIIEQGGVY 194 Query: 58 -LVGPTGVGKTAISRRLA 74 L+GPTGVGKT + +LA Sbjct: 195 ALIGPTGVGKTTTTAKLA 212 >gnl|CDD|173186 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 767 Score = 32.1 bits (73), Expect = 0.33 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 14/75 (18%) Query: 7 FSPREIVSELDRYIIGQQDAKRAVAIALRNRWRRQQLPADL-----RDELMPKN--ILLV 59 FS + + L+R +G D A+A W R +L L D L+ + + LV Sbjct: 139 FSGQLARALLERLPVGY-DRPAAMA------WIRNELATHLPVLRDEDALLAQGGVLALV 191 Query: 60 GPTGVGKTAISRRLA 74 GPTGVGKT + +LA Sbjct: 192 GPTGVGKTTTTAKLA 206 >gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional. Length = 506 Score = 31.9 bits (72), Expect = 0.35 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 16/57 (28%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARL 76 +IGQ+ KR + I N+LL+GP G GKT ++ R+ L Sbjct: 193 VIGQEQGKRGLEITAAG----------------GHNLLLIGPPGTGKTMLASRINGL 233 >gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases. Length = 163 Score = 32.0 bits (73), Expect = 0.36 Identities = 12/27 (44%), Positives = 16/27 (59%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFI 82 +L+G G GK+ I+ LA GA FI Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFI 27 >gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF; Provisional. Length = 388 Score = 31.8 bits (72), Expect = 0.38 Identities = 15/30 (50%), Positives = 19/30 (63%) Query: 49 DELMPKNILLVGPTGVGKTAISRRLARLAG 78 D L + +LVGPTGVGKT +LA + G Sbjct: 170 DNLKKRVFILVGPTGVGKTTTIAKLAAIYG 199 >gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed. Length = 394 Score = 31.4 bits (72), Expect = 0.43 Identities = 11/34 (32%), Positives = 17/34 (50%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKVEV 86 P N+L+ GP G GKT +++ +KV Sbjct: 55 PLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVY 88 >gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 484 Score = 31.5 bits (72), Expect = 0.46 Identities = 11/17 (64%), Positives = 14/17 (82%) Query: 58 LVGPTGVGKTAISRRLA 74 L+GPTGVGKT + +LA Sbjct: 261 LMGPTGVGKTTTTAKLA 277 >gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional. Length = 367 Score = 31.4 bits (71), Expect = 0.50 Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFT----EIGYVGRNVEQIIRDLVD 108 +L GP GVGKT +R LAR P F+ E+ N IR+L+D Sbjct: 42 LLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRNLID 98 >gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated. Length = 328 Score = 31.2 bits (71), Expect = 0.52 Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 3/34 (8%) Query: 41 QQLPADLRDELMPKNILLVGPTGVGKTAISRRLA 74 QQL R P LL GP G+GK A++ RLA Sbjct: 13 QQLAGRGR---HPHAYLLHGPAGIGKRALAERLA 43 >gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated. Length = 325 Score = 31.4 bits (71), Expect = 0.54 Identities = 11/26 (42%), Positives = 14/26 (53%) Query: 50 ELMPKNILLVGPTGVGKTAISRRLAR 75 E P L G G+GKTA +R A+ Sbjct: 18 ERRPNAWLFAGKKGIGKTAFARFAAQ 43 >gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional. Length = 345 Score = 31.3 bits (72), Expect = 0.55 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%) Query: 40 RQQLPADLRDELMPKN-ILLVGPTGVGKTAISRRLARLAGAPFI 82 R+ + L + ++L G TG GKT + + LA AGA + Sbjct: 127 RRFVIDTLEEAPAQFPLVVLGGNTGSGKTELLQALAN-AGAQVL 169 >gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed. Length = 337 Score = 31.1 bits (71), Expect = 0.61 Identities = 13/27 (48%), Positives = 16/27 (59%) Query: 49 DELMPKNILLVGPTGVGKTAISRRLAR 75 D ++L+ GP G GKTA R LAR Sbjct: 32 DSPNLPHLLVQGPPGSGKTAAVRALAR 58 >gnl|CDD|180779 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated. Length = 342 Score = 30.9 bits (70), Expect = 0.61 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 4/38 (10%) Query: 38 WRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 W R Q LR L P +LL G G+GK ++ LA+ Sbjct: 10 WNRLQ---ALRARL-PHALLLHGQAGIGKLDFAQHLAQ 43 >gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis. Length = 531 Score = 30.9 bits (70), Expect = 0.62 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 26/86 (30%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLARLA-- 77 IIGQ++ +A+ AL P P+++++ GP GVGKTA +R + A Sbjct: 67 IIGQEEGIKALKAALCG-------PN-------PQHVIIYGPPGVGKTAAARLVLEEAKK 112 Query: 78 --------GAPFIKVEVT--KFTEIG 93 GA F++++ T +F E G Sbjct: 113 NPASPFKEGAAFVEIDATTARFDERG 138 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 30.7 bits (69), Expect = 0.78 Identities = 11/27 (40%), Positives = 20/27 (74%) Query: 58 LVGPTGVGKTAISRRLARLAGAPFIKV 84 LVGP GVGKT++ + +A+ G ++++ Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRM 380 >gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der; Reviewed. Length = 712 Score = 30.5 bits (69), Expect = 0.80 Identities = 11/23 (47%), Positives = 17/23 (73%) Query: 60 GPTGVGKTAISRRLARLAGAPFI 82 GP GVGK+++SR LA+ G ++ Sbjct: 8 GPAGVGKSSVSRALAQYLGYAYL 30 >gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional. Length = 438 Score = 30.5 bits (69), Expect = 0.86 Identities = 13/32 (40%), Positives = 21/32 (65%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKV 84 PK ++L GP G GKT +++ +A A F++V Sbjct: 217 PKGVILYGPPGTGKTLLAKAVANETSATFLRV 248 >gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau. Length = 188 Score = 30.7 bits (70), Expect = 0.88 Identities = 13/36 (36%), Positives = 17/36 (47%) Query: 40 RQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 QQL L + L GP GVGK ++ LA+ Sbjct: 1 YQQLKRALEKGRLAHAYLFAGPEGVGKELLALALAK 36 >gnl|CDD|163168 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene. Length = 311 Score = 30.3 bits (69), Expect = 0.92 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVE 85 I+L G TG GKT + LA AGA + +E Sbjct: 130 IVLGGMTGSGKTELLHALAN-AGAQVLDLE 158 >gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine. Length = 287 Score = 30.4 bits (69), Expect = 0.94 Identities = 12/30 (40%), Positives = 20/30 (66%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVE 85 I ++GPT VGK+ ++ +LA+ A I V+ Sbjct: 2 IFIMGPTAVGKSQLAIQLAKKLNAEIISVD 31 >gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional. Length = 327 Score = 30.4 bits (69), Expect = 0.97 Identities = 11/27 (40%), Positives = 14/27 (51%) Query: 58 LVGPTGVGKTAISRRLARLAGAPFIKV 84 + G +G GKT R LA L G + V Sbjct: 13 VAGDSGCGKTTFLRGLADLLGEELVTV 39 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 30.3 bits (69), Expect = 1.00 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 10/56 (17%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 ++G + AK + W + + K +LL GP GVGKT+++ LA Sbjct: 16 VVGNEKAKEQL-REWIESWLKGK---------PKKALLLYGPPGVGKTSLAHALAN 61 >gnl|CDD|173382 PTZ00088, PTZ00088, adenylate kinase 1; Provisional. Length = 229 Score = 30.1 bits (68), Expect = 1.0 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 9/90 (10%) Query: 53 PKNILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIRDL 106 P I+L G GVGK + L++ I + E+ T I G+ +++++ Sbjct: 6 PLKIVLFGAPGVGKGTFAEILSKKENLKHINMGNILREEIKAKTTI---GKEIQKVVTSG 62 Query: 107 VDVAINIVRESRRDEVREQASINAEERILD 136 V N+V +DE+ + + ILD Sbjct: 63 NLVPDNLVIAIVKDEIAKVTDDCFKGFILD 92 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 29.9 bits (68), Expect = 1.4 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 54 KNILLVGPTGVGKTAISRRL 73 K I+L+G +G GKT +++ L Sbjct: 2 KKIMLIGRSGCGKTTLTQAL 21 >gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed. Length = 352 Score = 30.0 bits (68), Expect = 1.4 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 4/46 (8%) Query: 28 RAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRL 73 + + I++ + L LR+ K ++ GP+GVGK+++ RL Sbjct: 151 QPLFISVETGIGLEALLEQLRN----KITVVAGPSGVGKSSLINRL 192 >gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131 Score = 29.4 bits (67), Expect = 1.6 Identities = 13/32 (40%), Positives = 20/32 (62%) Query: 56 ILLVGPTGVGKTAISRRLARLAGAPFIKVEVT 87 +LL G G+ KT ++R LAR G F +++ T Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDFRRIQFT 33 >gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. Length = 512 Score = 29.7 bits (67), Expect = 1.7 Identities = 12/22 (54%), Positives = 16/22 (72%) Query: 53 PKNILLVGPTGVGKTAISRRLA 74 PK +LL GP G GKT I++ +A Sbjct: 216 PKGVLLYGPPGCGKTLIAKAVA 237 >gnl|CDD|151009 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB protein. This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilize the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724. Length = 89 Score = 29.3 bits (67), Expect = 2.1 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 5/50 (10%) Query: 350 KELMKTEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLED 399 ++ + GI L+ T+ + D LA+ + GAR L+ ++R +ED Sbjct: 18 QKRLAERGITLELTDAAKDWLAEKGYDPEY-----GARPLRRAIQREIED 62 >gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728). Length = 262 Score = 29.4 bits (66), Expect = 2.2 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 58 LVGPTGVGKTAISRRLARLAGAPFI 82 L GP G GKT ++ +AR P + Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRPVM 50 >gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional. Length = 491 Score = 29.0 bits (65), Expect = 2.4 Identities = 12/20 (60%), Positives = 17/20 (85%) Query: 52 MPKNILLVGPTGVGKTAISR 71 +P++ILLVG +GVGKT +R Sbjct: 34 IPQSILLVGASGVGKTTCAR 53 >gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional. Length = 205 Score = 28.9 bits (66), Expect = 2.5 Identities = 9/25 (36%), Positives = 17/25 (68%), Gaps = 2/25 (8%) Query: 51 LMPKNILLV--GPTGVGKTAISRRL 73 +M + +L+V GP+G GK+ + + L Sbjct: 1 MMRRGLLIVLSGPSGAGKSTLVKAL 25 >gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein. Length = 608 Score = 29.0 bits (65), Expect = 2.7 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 19/76 (25%) Query: 4 TFNFSPREIVSELDRYI---IGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVG 60 F E + +R I IGQ++A + A + + +N+LL+G Sbjct: 1 GIKFETTEEIPVPERLIDQVIGQEEAVEIIKKAAKQK----------------RNVLLIG 44 Query: 61 PTGVGKTAISRRLARL 76 GVGK+ +++ +A L Sbjct: 45 EPGVGKSMLAKAMAEL 60 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 28.9 bits (65), Expect = 2.7 Identities = 12/28 (42%), Positives = 18/28 (64%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFI 82 +++L GP GVGKT ++R +A A F Sbjct: 54 SLILYGPPGVGKTTLARIIANHTRAHFS 81 >gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional regulator; Reviewed. Length = 309 Score = 28.8 bits (65), Expect = 2.7 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%) Query: 42 QLPADLRDELMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTE 91 + R + I L+G G GK+ + R LA G PF VE+ + E Sbjct: 122 GMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPF--VELNREIE 169 >gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 374 Score = 28.9 bits (64), Expect = 2.8 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 7/44 (15%) Query: 38 WRRQQLPADL-----RDELMPKN--ILLVGPTGVGKTAISRRLA 74 W + L A+L D LM + L+GPTGVGKT + +LA Sbjct: 115 WAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAKLA 158 >gnl|CDD|184585 PRK14239, PRK14239, phosphate transporter ATP-binding protein; Provisional. Length = 252 Score = 28.6 bits (64), Expect = 2.9 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%) Query: 50 ELMPKNIL-LVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108 + P I L+GP+G GK+ + R + R+ + EVT I Y G N+ D VD Sbjct: 27 DFYPNEITALIGPSGSGKSTLLRSINRMND---LNPEVTITGSIVYNGHNIYSPRTDTVD 83 Query: 109 V 109 + Sbjct: 84 L 84 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 28.7 bits (65), Expect = 3.1 Identities = 12/17 (70%), Positives = 15/17 (88%) Query: 54 KNILLVGPTGVGKTAIS 70 KN L+V PTG+GKTAI+ Sbjct: 30 KNTLVVLPTGLGKTAIA 46 >gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 361 Score = 28.4 bits (64), Expect = 3.4 Identities = 8/21 (38%), Positives = 13/21 (61%) Query: 56 ILLVGPTGVGKTAISRRLARL 76 + L+GP G GK+++ L R Sbjct: 81 LYLLGPVGGGKSSLVECLKRG 101 >gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid. Length = 191 Score = 28.4 bits (64), Expect = 3.4 Identities = 11/31 (35%), Positives = 16/31 (51%) Query: 45 ADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 +D + P +LL G G GKT ++R L Sbjct: 4 SDKPPQERPVAVLLGGQPGAGKTELARALLE 34 >gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. Length = 355 Score = 28.7 bits (65), Expect = 3.5 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 15/57 (26%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQL-PADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 +IGQ+ + L+N + ++ A L GP G GKT+I+R A+ Sbjct: 16 VIGQE----HIVQTLKNAIKNGRIAHA----------YLFSGPRGTGKTSIARIFAK 58 >gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional. Length = 585 Score = 28.6 bits (64), Expect = 3.6 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 15/57 (26%) Query: 33 ALRNRWRRQQLPAD----------LRDELMPKNI----LLVGPTGVGKTAISRRLAR 75 L +WR Q A+ LR+ + + L GP GVGKT+ +R LA+ Sbjct: 5 VLYRKWRSQTF-AELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAK 60 >gnl|CDD|152439 pfam12004, DUF3498, Domain of unknown function (DUF3498). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with pfam00616, pfam00168. This domain has two conserved sequence motifs: DLQ and PLSFQNP. Length = 489 Score = 28.1 bits (62), Expect = 4.0 Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 3/36 (8%) Query: 116 ESRRDEVREQASINAEERILDALVGKTAT---SNTR 148 E ++D QA ++++++I+DA + A+ +NTR Sbjct: 442 ELKKDHADMQAVVDSKQKIIDAQERRIASLDAANTR 477 >gnl|CDD|181814 PRK09389, PRK09389, (R)-citramalate synthase; Provisional. Length = 488 Score = 28.4 bits (64), Expect = 4.2 Identities = 27/81 (33%), Positives = 35/81 (43%), Gaps = 18/81 (22%) Query: 107 VDVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEID 166 VD AIN VR++ + A I EE +DA+ G T EV KL G D+ Sbjct: 415 VDAAINAVRKA----LSGVADIELEEYHVDAITGGTDALVEVEV---KLSRG---DRV-- 462 Query: 167 IEVADTSSDISNFDIPGGASV 187 + V +DI ASV Sbjct: 463 VTVRGADADIIM------ASV 477 >gnl|CDD|184809 PRK14738, gmk, guanylate kinase; Provisional. Length = 206 Score = 28.2 bits (63), Expect = 4.3 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%) Query: 45 ADLRDELMPKNILLV--GPTGVGKTAISRRLARLAGAPF 81 K +L+V GP+GVGK A+ R+ R PF Sbjct: 3 NPWLFNKPAKPLLVVISGPSGVGKDAVLARM-RERKLPF 40 >gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional. Length = 614 Score = 28.2 bits (63), Expect = 4.5 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 13/56 (23%) Query: 20 IIGQQDAKRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 ++GQ A+ L+N +L L GP GVGKT +R A+ Sbjct: 19 VVGQ----EALTTTLKNAIATNKLA---------HAYLFCGPRGVGKTTCARIFAK 61 >gnl|CDD|181017 PRK07529, PRK07529, AMP-binding domain protein; Validated. Length = 632 Score = 28.0 bits (63), Expect = 4.5 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 16/67 (23%) Query: 119 RDEVREQASINAEERILDAL----VGKT--------ATSNTREVFRKKLRDGEISDKEID 166 RD + E+A++ RILDAL VGK A R V R LRD + + +D Sbjct: 532 RDHIAERAAVPKHVRILDALPKTAVGKIFKPALRRDAI---RRVLRAALRDAGVEAEVVD 588 Query: 167 IEVADTS 173 + V D Sbjct: 589 V-VEDGR 594 >gnl|CDD|162762 TIGR02208, lipid_A_msbB, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase. This family consists of MsbB in E. coli and closely related proteins in other species. MsbB is homologous to HtrB (TIGR02207) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars. Length = 305 Score = 28.2 bits (63), Expect = 4.6 Identities = 8/34 (23%), Positives = 17/34 (50%) Query: 196 FSKVMGSGRKKKIRMSVQKCYPELMRDESDRLID 229 F + + + R+++ C+PE E + +ID Sbjct: 45 FVGPIAKKPRGRARINLSACFPEKSEAERETIID 78 >gnl|CDD|184589 PRK14248, PRK14248, phosphate ABC transporter ATP-binding protein; Provisional. Length = 268 Score = 28.0 bits (62), Expect = 5.1 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 12/62 (19%) Query: 58 LVGPTGVGKTAISRRLARLAGA-PFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRE 116 L+GP+G GK+ R + R+ P + E EI Y G N+ +D IN+V Sbjct: 52 LIGPSGCGKSTFLRSINRMNDLIPSARSE----GEILYEGLNI-------LDSNINVVNL 100 Query: 117 SR 118 R Sbjct: 101 RR 102 >gnl|CDD|178749 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional. Length = 1153 Score = 27.9 bits (62), Expect = 5.1 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 24/106 (22%) Query: 60 GPTGVGKTAISRRL-----ARLAGAPFI-KVEVTKFTEIGYVGRNVEQI----------- 102 G +G+GKT I+R L + + FI + ++K EI Y N + Sbjct: 214 GSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEI-YSSANPDDYNMKLHLQRAFL 272 Query: 103 --IRDLVDVAINIVRESRRDEVREQASINA----EERILDALVGKT 142 I D D+ I + + I ++ +LDAL G+T Sbjct: 273 SEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQT 318 >gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional. Length = 484 Score = 28.0 bits (62), Expect = 5.3 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 57 LLVGPTGVGKTAISRRLAR 75 + GP GVGKT I+R LA+ Sbjct: 44 IFFGPRGVGKTTIARILAK 62 >gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated. Length = 709 Score = 27.8 bits (61), Expect = 5.4 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 57 LLVGPTGVGKTAISRRLAR 75 LL G GVGKT I+R LA+ Sbjct: 42 LLTGTRGVGKTTIARILAK 60 >gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase. Length = 261 Score = 27.9 bits (62), Expect = 5.6 Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%) Query: 53 PKNILLV--GPTGVGKTAISRRLARLAGAPFI 82 +N+ V G GVGK + RL++L G P I Sbjct: 27 GRNVNWVFLGCPGVGKGTYASRLSKLLGVPHI 58 >gnl|CDD|183705 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF; Provisional. Length = 559 Score = 27.7 bits (61), Expect = 5.6 Identities = 12/21 (57%), Positives = 14/21 (66%) Query: 56 ILLVGPTGVGKTAISRRLARL 76 I LVGPTG GKT +LA+ Sbjct: 353 IALVGPTGAGKTTTIAKLAQR 373 >gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional. Length = 700 Score = 27.9 bits (62), Expect = 5.7 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 57 LLVGPTGVGKTAISRRLAR 75 L G GVGKT +SR LA+ Sbjct: 42 LFTGTRGVGKTTLSRILAK 60 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 27.8 bits (62), Expect = 5.7 Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 16/57 (28%) Query: 20 IIGQQDA-KRAVAIALRNRWRRQQLPADLRDELMPKNILLVGPTGVGKTAISRRLAR 75 I+G +DA R IA RD MP N++L GP G GKT LA Sbjct: 15 IVGNEDAVSRLQVIA--------------RDGNMP-NLILSGPPGTGKTTSILALAH 56 >gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. Length = 395 Score = 27.7 bits (62), Expect = 6.0 Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 2/30 (6%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGA--PF 81 + +L+ GP G GKTA++ +++ G PF Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPF 80 >gnl|CDD|177388 PHA02554, 13, neck protein; Provisional. Length = 311 Score = 27.8 bits (62), Expect = 6.1 Identities = 18/51 (35%), Positives = 21/51 (41%), Gaps = 16/51 (31%) Query: 66 KTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINIVRE 116 K I RRL GAP I VEVT E I D + A+ + E Sbjct: 12 KDYILRRL----GAPIINVEVT------------EDQIYDCIQRALELYGE 46 >gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated. Length = 329 Score = 27.6 bits (62), Expect = 6.1 Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 4/24 (16%) Query: 54 KNILLVGPTGVGKT----AISRRL 73 +N+L G TG GKT I++ L Sbjct: 184 ENLLFYGNTGTGKTFLSNCIAKEL 207 >gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated. Length = 365 Score = 27.7 bits (62), Expect = 6.2 Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%) Query: 57 LLVGPTGVGKTAISRRLAR--LAGAP 80 L+ GP G+GK ++ R+AR LA P Sbjct: 45 LIGGPQGIGKATLAYRMARFLLATPP 70 >gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11; Provisional. Length = 344 Score = 27.6 bits (61), Expect = 6.4 Identities = 11/18 (61%), Positives = 14/18 (77%) Query: 56 ILLVGPTGVGKTAISRRL 73 +LL GPTG GKT +S+ L Sbjct: 165 MLLCGPTGSGKTTMSKTL 182 >gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP. Length = 180 Score = 27.4 bits (62), Expect = 7.0 Identities = 8/18 (44%), Positives = 14/18 (77%) Query: 56 ILLVGPTGVGKTAISRRL 73 I++ GP+GVGK+ + + L Sbjct: 4 IVISGPSGVGKSTLVKAL 21 >gnl|CDD|184728 PRK14530, PRK14530, adenylate kinase; Provisional. Length = 215 Score = 27.4 bits (61), Expect = 7.0 Identities = 10/24 (41%), Positives = 12/24 (50%) Query: 51 LMPKNILLVGPTGVGKTAISRRLA 74 + ILL+G G GK S LA Sbjct: 1 MSQPRILLLGAPGAGKGTQSSNLA 24 >gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM). Length = 566 Score = 27.4 bits (61), Expect = 7.0 Identities = 10/22 (45%), Positives = 15/22 (68%) Query: 54 KNILLVGPTGVGKTAISRRLAR 75 ++IL+ G TG GK+ R+L R Sbjct: 177 QHILIHGTTGSGKSVAIRKLLR 198 >gnl|CDD|183360 PRK11889, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 436 Score = 27.3 bits (60), Expect = 7.0 Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 16/102 (15%) Query: 54 KNILLVGPTGVGKTAISRRLA-----RLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVD 108 + I L+GPTGVGKT ++A + FI + ++ + + V+ I +++ Sbjct: 242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA 301 Query: 109 VAINIVRESRRDEVREQASIN--AEERILDALVGKTATSNTR 148 V RDE ++ EE +D ++ TA N R Sbjct: 302 V---------RDEAAMTRALTYFKEEARVDYILIDTAGKNYR 334 >gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional. Length = 618 Score = 27.4 bits (61), Expect = 7.3 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 57 LLVGPTGVGKTAISRRLAR 75 L G GVGKT +SR LA+ Sbjct: 42 LFTGTRGVGKTTVSRILAK 60 >gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related. Length = 585 Score = 27.5 bits (61), Expect = 7.4 Identities = 20/106 (18%), Positives = 39/106 (36%), Gaps = 11/106 (10%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYVGRNVEQIIRDLVDVAINI 113 + + +VGPTG GKT + L R V +I G ++ + R+ + +I Sbjct: 362 QTVAIVGPTGAGKTTLINLLQR--------VYDPTVGQILIDGIDINTVTRESLRKSIAT 413 Query: 114 VRESR---RDEVREQASINAEERILDALVGKTATSNTREVFRKKLR 156 V + +RE + E + + + + K+ Sbjct: 414 VFQDAGLFNRSIRENIRLGREGATDEEVYEAAKAAAAHDFILKRSN 459 >gnl|CDD|162313 TIGR01351, adk, adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason. Length = 210 Score = 27.6 bits (62), Expect = 7.5 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 13/72 (18%) Query: 55 NILLVGPTGVGKTAISRRLARLAGAPFIKV------EVTKFTEIGYVGRNVEQIIR--DL 106 ++L+GP G GK ++R+A G P I E+ T + G+ ++ + +L Sbjct: 1 RLVLLGPPGSGKGTQAKRIAEKYGLPHISTGDLLRAEIKAGTPL---GKKAKEYMEKGEL 57 Query: 107 V--DVAINIVRE 116 V ++ +V+E Sbjct: 58 VPDEIVNQLVKE 69 >gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional. Length = 457 Score = 27.5 bits (61), Expect = 7.6 Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 3/33 (9%) Query: 55 NILLVGPTGVGKTAISRRL---ARLAGAPFIKV 84 ++L+ G +G GK I+R + +R A PFIKV Sbjct: 168 SVLISGESGTGKELIARAIHYNSRRAKGPFIKV 200 >gnl|CDD|130495 TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related. Length = 198 Score = 27.3 bits (61), Expect = 7.9 Identities = 8/29 (27%), Positives = 11/29 (37%) Query: 24 QDAKRAVAIALRNRWRRQQLPADLRDELM 52 + AL WR++QL LM Sbjct: 23 AELYGGRGEALSQLWRQKQLEYSWLRTLM 51 >gnl|CDD|179573 PRK03372, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional. Length = 306 Score = 27.2 bits (61), Expect = 8.2 Identities = 13/26 (50%), Positives = 14/26 (53%) Query: 64 VGKTAISRRLARLAGAPFIKVEVTKF 89 V + A RLARL APF V KF Sbjct: 269 VRRGATPVRLARLDSAPFTDRLVRKF 294 >gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional. Length = 248 Score = 27.2 bits (61), Expect = 8.3 Identities = 16/30 (53%), Positives = 18/30 (60%), Gaps = 4/30 (13%) Query: 50 ELMPKNIL-LVGPTGVGKTAISRRLARLAG 78 E+ IL LVGP G GK S LAR+AG Sbjct: 18 EVRAGEILHLVGPNGAGK---STLLARMAG 44 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 27.1 bits (60), Expect = 8.6 Identities = 7/16 (43%), Positives = 11/16 (68%) Query: 54 KNILLVGPTGVGKTAI 69 ++++L PTG GKT Sbjct: 25 RDVILAAPTGSGKTLA 40 >gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed. Length = 251 Score = 27.4 bits (61), Expect = 8.7 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%) Query: 40 RQQLPADLRDELMPKNIL-LVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGYV 95 ++++ +D+ EL P IL L+GP G GK+ + R + L ++ IGYV Sbjct: 16 QRRVLSDVSLELKPGKILTLLGPNGAGKSTLVRVVLGLVAPDEGVIKRNGKLRIGYV 72 >gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. Length = 164 Score = 27.1 bits (61), Expect = 9.1 Identities = 8/20 (40%), Positives = 14/20 (70%) Query: 56 ILLVGPTGVGKTAISRRLAR 75 I+L+G +GVGK+++ R Sbjct: 3 IILIGDSGVGKSSLLSRFTD 22 >gnl|CDD|152127 pfam11691, DUF3288, Protein of unknown function (DUF3288). This family of proteins with unknown function appears to be restricted to Cyanobacteria. Length = 90 Score = 27.2 bits (61), Expect = 9.6 Identities = 10/27 (37%), Positives = 16/27 (59%) Query: 385 GARRLQTVMERVLEDISFSASDLQEKT 411 GA LQ +E+VL+ + +L E+T Sbjct: 43 GAEDLQRDLEKVLKLWGLTEEELFERT 69 >gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF; Provisional. Length = 432 Score = 27.2 bits (60), Expect = 9.6 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 5/53 (9%) Query: 54 KNILLVGPTGVGKTAISRRLARLAGAPFIKV--EVTKFTEIGYVGRNVEQIIR 104 K + VGPTG GKT +A+LA F+ + V+ +T Y +EQ+ R Sbjct: 224 KVVFFVGPTGSGKTT---SIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKR 273 >gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit; Provisional. Length = 351 Score = 27.0 bits (60), Expect = 9.8 Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 5/36 (13%) Query: 58 LVGPTGVGKTAISRRLARL----AGAPFIKVE-VTK 88 L+GP+G GKT + R +A L G FI E VT Sbjct: 37 LLGPSGCGKTTVLRLVAGLEKPTEGQIFIDGEDVTH 72 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.319 0.137 0.376 Gapped Lambda K H 0.267 0.0662 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,232,501 Number of extensions: 494314 Number of successful extensions: 1646 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1625 Number of HSP's successfully gapped: 192 Length of query: 437 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 341 Effective length of database: 3,920,105 Effective search space: 1336755805 Effective search space used: 1336755805 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 (26.6 bits)