RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780725|ref|YP_003065138.1| response regulator receiver protein [Candidatus Liberibacter asiaticus str. psy62] (427 letters) >gnl|CDD|163527 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein. Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria. Length = 322 Score = 46.6 bits (111), Expect = 1e-05 Identities = 41/172 (23%), Positives = 69/172 (40%), Gaps = 18/172 (10%) Query: 147 SAIFTPQEEGKGSSGCSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLAD-------L 199 + ++ + G ++ IG RGG G+ST+A A + A + TLL D L Sbjct: 79 VELLADLDQSPPARGVVVAVIGGRGGAGASTLAAALALAAARH-GLRTLLVDADPWGGGL 137 Query: 200 DLPYGTANINFDKDPINSISDAIYPVGRID-KAFVSRLPVFYAENLSILTAPAMLSRTYD 258 DL G ++ + P S + GR+ A LP LS+L+ + Sbjct: 138 DLLLGAEDVPGLRWPDLSQAR-----GRLPAGALRDALPR--RGGLSVLSWGR--AVGAA 188 Query: 259 FDEKMIVPVLDILEQIFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAG 310 + VLD + LV++D+P + L +D V++ D+ Sbjct: 189 LPPAAVRAVLDAARRGGDLVVVDLPRRLTPAAETALESADLVLVVVPADVRA 240 >gnl|CDD|131023 TIGR01968, minD_bact, septum site-determining protein MinD. This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model. Length = 261 Score = 43.1 bits (102), Expect = 2e-04 Identities = 59/269 (21%), Positives = 126/269 (46%), Gaps = 34/269 (12%) Query: 170 RGGVGSSTIAHNCAFSIAS------VFAMETLLADLDLPYGTAN-INFDKDPINSISDAI 222 +GGVG +T N ++A + + L +LDL G N I + + D + Sbjct: 10 KGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDLLLGLENRIVYT------LVDVV 63 Query: 223 YPVGRIDKAFVS--RLPVFYAENLSILTAPAMLSRT-YDFDEKMIVPVLDILEQIFPLVI 279 R+ +A + RL +NL +L PA +R + + +++ L++ F VI Sbjct: 64 EGECRLQQALIKDKRL-----KNLYLL--PASQTRDKDAVTPEQMKKLVNELKEEFDYVI 116 Query: 280 LDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLVLNQVK 339 +D P S + + +D+ ++ T+ +++ +R++ +I +L+ + +L++N+++ Sbjct: 117 IDCPAGIESGFRNAVAPADEAIVVTTPEVSAVRDADRVIGLLEA--KGIEKIHLIVNRLR 174 Query: 340 TP--KKPE-ISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLVDF 396 KK + +S+ D L I +IP D A+ +S N G+ + ++ KS + Sbjct: 175 PEMVKKGDMLSVDDVLEILSIPLIGVIPEDEAII-VSTNKGEPV-VLNDKSRAGKAFENI 232 Query: 397 SRVLMGR----VTVSKPQSAMYTKIKKIF 421 +R ++G ++ + + +IK+ F Sbjct: 233 ARRILGEEVPFEDLTTQKKGFFARIKRFF 261 >gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional. Length = 270 Score = 34.5 bits (79), Expect = 0.054 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 28/234 (11%) Query: 162 CSISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANINF----DKDPINS 217 I +GGVG +T + A +A +T++ D D+ G N++ ++ + Sbjct: 3 RIIVVTSGKGGVGKTTSSAAIATGLAQK-GKKTVVIDFDI--GLRNLDLIMGCERRVVYD 59 Query: 218 ISDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLSRTYDFD----EKMIVPVLDILEQ 273 + I +++A + ENL IL A S+T D D E + + D+ Sbjct: 60 FVNVIQGDATLNQALIKDK---RTENLYILPA----SQTRDKDALTREGVAKVLDDLKAM 112 Query: 274 IFPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVL-KKLRPADK--- 329 F ++ D P + L +D+ +ITT+ +++ +R+S ++ +L K R A+ Sbjct: 113 DFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEE 172 Query: 330 --PPYLVL---NQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGK 378 +L+L N + + +S+ D L I +IP D +V ++N G+ Sbjct: 173 PIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVL-RASNQGE 225 >gnl|CDD|163238 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined. Length = 246 Score = 31.9 bits (73), Expect = 0.34 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 7/40 (17%) Query: 164 ISFIGSRGGVGSSTIAHNCAFSIASVFAM---ETLLADLD 200 I+ +G +GGVG +T+ N +AS + L DLD Sbjct: 4 IAIVGVKGGVGKTTLTAN----LASALKLLGEPVLAIDLD 39 >gnl|CDD|167016 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional. Length = 1809 Score = 31.3 bits (71), Expect = 0.49 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 2/33 (6%) Query: 220 DAIYPVGRIDKAFVSRLPVFYAENLSILTAPAM 252 D IY GR K ++S LP F+A L L P++ Sbjct: 45 DTIYAAGR--KRYLSTLPSFFATTLDSLPDPSV 75 >gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal. This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown. Length = 251 Score = 30.1 bits (68), Expect = 1.2 Identities = 51/248 (20%), Positives = 99/248 (39%), Gaps = 25/248 (10%) Query: 163 SISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTANI----NFDKDPINSI 218 I+ +GG G +TI N ++A + L D D+ AN+ + P+ ++ Sbjct: 2 IITIASGKGGTGKTTITANLGVALAK-LGKKVLALDADI--TMANLELILGMEDKPV-TL 57 Query: 219 SDAIYPVGRIDKAFVSRLPVFYAENLSILTAPAMLS----RTYDFDEKMIVPVLDILEQI 274 D + I A Y + PA +S R D D+ + VL + Sbjct: 58 HDVLAGEADIKDA-------IYEGPFGVKVIPAGVSLEGLRKADPDK--LEDVLKEIIDD 108 Query: 275 FPLVILDVPHVWNSWTQEVLTLSDKVVITTSLDLAGLRNSKNLIDVLKKLRPADKPPYLV 334 +++D P L +D++++ + +++ + ++ V +KL +V Sbjct: 109 TDFLLIDAPAGLERDAVTALAAADELLLVVNPEISSITDALKTKIVAEKL--GTAILGVV 166 Query: 335 LNQVKTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGKMIHEVDPKSAIANLLV 394 LN+V T K E+ + L + ++P D V +A G+ + +P S A + Sbjct: 167 LNRV-TRDKTELGREEIETILEVPVLGVVPEDPEVRRAAA-FGEPVVIYNPNSPAAQAFM 224 Query: 395 DFSRVLMG 402 + + L G Sbjct: 225 ELAAELAG 232 >gnl|CDD|179762 PRK04169, PRK04169, geranylgeranylglyceryl phosphate synthase-like protein; Reviewed. Length = 232 Score = 29.4 bits (67), Expect = 1.6 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 8/74 (10%) Query: 85 TKVDSREVLSALEPLAEVCDSGTKVIVIGDTNDVSLYR--ALISNHVSEY----LIEPLS 138 T +D + L E L +C+SGT I++G ++ V+ L+ + EY ++ P + Sbjct: 12 TLLDPDKPLPD-EALEAICESGTDAIIVGGSDGVTEENVDELVKA-IKEYDLPVILFPGN 69 Query: 139 VADIINSISAIFTP 152 + I A P Sbjct: 70 IEGISPGADAYLFP 83 >gnl|CDD|180603 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed. Length = 304 Score = 28.7 bits (65), Expect = 3.0 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 5/58 (8%) Query: 58 MRITRGSIAEAVSCFSDSS---TPDLIIVQTKVDSREVLSALEPLAEVCDSGTKVIVI 112 +R+ G I V D + DL+I+ K + +AL LA + T V+ + Sbjct: 44 LRLEDGEITVPVLAADDPAELGPQDLVILAVKAYQ--LPAALPSLAPLLGPDTPVLFL 99 >gnl|CDD|182700 PRK10752, PRK10752, sulfate transporter subunit; Provisional. Length = 329 Score = 28.6 bits (64), Expect = 3.1 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 220 DAIYPVGRIDKAFVSRLP 237 DAI GRIDK ++ RLP Sbjct: 89 DAIAERGRIDKNWIKRLP 106 >gnl|CDD|134018 PHA02518, PHA02518, ParA-like protein; Provisional. Length = 211 Score = 28.3 bits (63), Expect = 4.0 Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%) Query: 164 ISFIGSRGGVGSSTIAHNCAFSIASVFAMETLLADLDLPYGTA 206 I+ + +GG G +T+A N A + + + LL DLD P G++ Sbjct: 3 IAVLNQKGGAGKTTVATNLASWLHADGH-KVLLVDLD-PQGSS 43 >gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed. Length = 292 Score = 28.1 bits (64), Expect = 4.3 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 10/75 (13%) Query: 320 VLKKLRPADKPPYLVLNQV-KTPKKPEISISDFCAPLGITPSAIIPFDGAVFGMSANSGK 378 +L+KL+ P LVLN++ K E+ PL S ++ F + +SA G Sbjct: 105 ILEKLKKVKTPVILVLNKIDLVKDKEEL------LPLLEELSELMDFA-EIVPISALKGD 157 Query: 379 MIHEVDPKSAIANLL 393 + E+ IA L Sbjct: 158 NVDEL--LDVIAKYL 170 >gnl|CDD|162018 TIGR00745, apbA_panE, 2-dehydropantoate 2-reductase. This model describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes (TIGR00222, TIGR00018, TIGR00223). The gene encoding this enzyme is designated apbA in Salmonella typhimurium and panE in Escherichia coli; this protein functions as a monomer and functions in the alternative pyrimidine biosynthetic, or APB, pathway, used to synthesize the pyrimidine moiety of thiamine. Note, synthesis of the pyrimidine moiety of thiamine occurs either via the first five steps in de novo purine biosynthesis, which uses the pur gene products, or through the APB pathway. Note that this family includes both NADH and NADPH-dependent enzymes, and enzymes with broad specificity, such as a D-mandelate dehydrogease that is also a 2-dehydropantoate 2-reductase. Length = 293 Score = 27.7 bits (62), Expect = 5.9 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%) Query: 67 EAVSCFSDSSTPDLIIVQTKV-DSREVLSALEPLAEVCDSGTKVIVI 112 A + + DL+I+ K + E + L PL TKV+ + Sbjct: 49 SAATSPEELPPADLVIITVKAYQTEEAAALLLPLI---GKNTKVLFL 92 >gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated. Length = 1437 Score = 27.1 bits (61), Expect = 8.4 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 166 FIGSRGGVGSSTIAH 180 +GSRG VGSS +A Sbjct: 881 LVGSRGSVGSSFVAT 895 >gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein. Length = 214 Score = 27.2 bits (61), Expect = 9.1 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 10/65 (15%) Query: 62 RGSIAEAVSCFSDSSTPDLIIVQT---KVDSREVLSALEPLAEVCDSGTKVIVIGDTNDV 118 R +IA A+ ++P L++ +D L+ L + GT VIV T+D+ Sbjct: 145 RVAIARAIV-----NSPPLLLADEPTGNLDPDLSERILDLLKRLNKRGTTVIVA--THDL 197 Query: 119 SLYRA 123 SL Sbjct: 198 SLVDR 202 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 0.135 0.386 Gapped Lambda K H 0.267 0.0715 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,816,217 Number of extensions: 440980 Number of successful extensions: 834 Number of sequences better than 10.0: 1 Number of HSP's gapped: 832 Number of HSP's successfully gapped: 20 Length of query: 427 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 331 Effective length of database: 3,920,105 Effective search space: 1297554755 Effective search space used: 1297554755 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)