RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781033|ref|YP_003065446.1| HemY domain-containing protein [Candidatus Liberibacter asiaticus str. psy62] (492 letters) >gnl|CDD|148680 pfam07219, HemY_N, HemY protein N-terminus. This family represents the N-terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. This is a membrane protein involved in a late step of protoheme IX synthesis. Length = 134 Score = 68.1 bits (167), Expect = 5e-12 Identities = 33/134 (24%), Positives = 59/134 (44%), Gaps = 3/134 (2%) Query: 1 MLRLIRYFFVISLV-ICSFIIVSHYPEDVSITWGNRLYRTSPFVILSILYFFLFAWILLF 59 MLR++ + F++ L+ + ++ P V I++G TS +L L LL Sbjct: 1 MLRVLLFLFLVLLLGLFGGAWLAGQPGYVVISYGGYRIETSLTFAAILLLAVLAVLFLLE 60 Query: 60 AVSRFFLSCPAMLFHMLHKRNYDKGYKALYTGLMSIAAHNIPLARKMHSYVSQQHTFHNE 119 + R + P + +R +G KAL GL+++A + LA ++ ++ Sbjct: 61 WLLRLIIRLPRRVRRYFRRRKRRRGRKALSEGLLALAEGDWALAERLARKAAELE--DQP 118 Query: 120 YLVYLLEVQIALAE 133 L LL + A AE Sbjct: 119 PLALLLAARAAQAE 132 >gnl|CDD|163072 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator. Length = 899 Score = 42.8 bits (101), Expect = 2e-04 Identities = 39/197 (19%), Positives = 83/197 (42%), Gaps = 12/197 (6%) Query: 168 GDLNSAQRYATKALDISPDAPWVTEAVVQQYVLAKEWSRAITFLNQKKKNAKEWNRNRAI 227 GD +A++ KAL + V + + Y+L ++ + + L K E A Sbjct: 70 GDYAAAEKELRKALSLGYPKNQVLPLLARAYLLQGKFQQVLDELPGKTLLDDE---GAAE 126 Query: 228 LLIARSLENADKGDMIASYHDAIESLKLCDNSIMASICAAKSLISQNKKRKAEVILEKIW 287 LL R L G + + ++L + S+ A + A+ +++N+ +A +++++ Sbjct: 127 LLALRGLAYLGLGQLELAQKSYEQALAIDPRSLYAKLGLAQLALAENRFDEARALIDEVL 186 Query: 288 KVNPHPEIA-NIYTHLL-----SENTVGKLKRALRLEEINKESVESLVIVSKIALEMGSI 341 +P A + LL E + ++A+ + + L+ ++ I +E G Sbjct: 187 TADPGNVDALLLKGDLLLSLGNIELALAAYRKAI---ALRPNNPAVLLALATILIEAGEF 243 Query: 342 DQAHAKAMLAMKIAPRK 358 ++A A +K AP Sbjct: 244 EEAEKHADALLKKAPNS 260 Score = 32.4 bits (74), Expect = 0.30 Identities = 42/217 (19%), Positives = 87/217 (40%), Gaps = 12/217 (5%) Query: 166 RIGDLNSAQRYATKALDISPDAPWVTEAVVQQYVLAKEWSRAITFLNQKKKNAKEWNRNR 225 R+G ++ A + AL + PD P + + Y+ ++ +A +L + + E R Sbjct: 341 RLGRVDEAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKAAEYLAKATELDPENAAAR 400 Query: 226 AILLIARSLENADKGDMIASYHDAIESLKLCDNSIMASICAAKSLISQNKKRKAEVILEK 285 L I++ + D + IA A +L A + S + + KA +K Sbjct: 401 TQLGISKLSQG-DPSEAIADLETAA---QLDPELGRADLLLILSYLRSGQFDKALAAAKK 456 Query: 286 IWKVNPHPEIANIYTHL----LSENTVGKLKRALRLE-EINKESVESLVIVSKIALEMGS 340 + K P+ A+++ L L + + K + A I + + +++I ++ G+ Sbjct: 457 LEK--KQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGN 514 Query: 341 IDQAHAKAMLAMKIAPR-KEIFLLLAQIEQANSHNTD 376 D A + + I P+ L LA + + + Sbjct: 515 PDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEE 551 >gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with one the E. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the divergent clade of putative ThiF proteins such found in Campylobacter. Length = 200 Score = 35.2 bits (81), Expect = 0.042 Identities = 32/113 (28%), Positives = 48/113 (42%), Gaps = 25/113 (22%) Query: 271 ISQNKKRKAEVILEKIWKVNPHPEIANIYTHLLSENTVGKLKRALRLEEINKESVESLVI 330 SQ + K E + E I ++NP+ EI Y E+I +E+++ Sbjct: 68 ASQVGEPKTEALKENISEINPYTEI-EAYD-----------------EKITEENIDKFFK 109 Query: 331 VSKIALEMGSIDQAHAKAMLA---MKIAPRKEIFLL--LAQIEQANSHNTDKI 378 + I E + D A AKAML ++ K + LA + ANS T KI Sbjct: 110 DADIVCE--AFDNAEAKAMLVNAVLEKYKDKYLIAASGLAGYDDANSIKTRKI 160 >gnl|CDD|168663 PRK06756, PRK06756, flavodoxin; Provisional. Length = 148 Score = 31.0 bits (70), Expect = 0.73 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 11/88 (12%) Query: 217 NAKEWNRNRAILLIARSLENADKGDMIASYHDAIESLKL----------CDNSIMASICA 266 A + I+L A + + D D ++DA++S+ L CD++ A Sbjct: 43 EASILEQYDGIILGAYTWGDGDLPDDFLDFYDAMDSIDLTGKKAAVFGSCDSAYPKYGVA 102 Query: 267 AKSLISQNKKRKAEVILEKIWKVNPHPE 294 LI + ++R A V+LE + KV PE Sbjct: 103 VDILIEKLQERGAAVVLEGL-KVELTPE 129 >gnl|CDD|182101 PRK09835, PRK09835, sensor kinase CusS; Provisional. Length = 482 Score = 29.7 bits (67), Expect = 1.5 Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%) Query: 38 RTSPFVILS-ILYFFLFAWILLFAVSRFF 65 R + F+ L+ I FF F WI++ +V F Sbjct: 15 RLTFFISLATIAAFFAFTWIMIHSVKVHF 43 >gnl|CDD|184064 PRK13461, PRK13461, F0F1 ATP synthase subunit B; Provisional. Length = 159 Score = 29.6 bits (67), Expect = 2.1 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%) Query: 271 ISQNKKRKAEVILEKIWKVNPHPEIANIYTHLLSENTVGKLKRALRLEEINKESVESLVI 330 I + K KAE + E+I K H E I + + ++ EI ++V+ V+ Sbjct: 76 IVEEYKSKAENVYEEIVK-EAHEEADLI---IERAKLEAQREKEKAEYEIKNQAVDLAVL 131 Query: 331 VSKIALEMGSIDQA 344 +S ALE SID++ Sbjct: 132 LSSKALE-ESIDES 144 >gnl|CDD|131573 TIGR02521, type_IV_pilW, type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain. Length = 234 Score = 28.8 bits (65), Expect = 3.1 Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 10/100 (10%) Query: 117 HNEYLVYLLEV-QIALAERQYNIAHEKLEMML--QIPATREFAVYSLYFESCRIGDLNSA 173 N Y +L + + A +Q+ A +E L Q + E A + GD + A Sbjct: 102 LNNYGTFLCQQGKYEQAMQQFEQA---IEDPLYPQPARSLENAGLCAL----KAGDFDKA 154 Query: 174 QRYATKALDISPDAPWVTEAVVQQYVLAKEWSRAITFLNQ 213 ++Y T+AL I P P + + Y L ++ A +L + Sbjct: 155 EKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLER 194 Score = 28.8 bits (65), Expect = 3.2 Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 26/122 (21%) Query: 127 VQIALA--ER-QYNIAHEKLEMMLQIPATREFA--VYSLYFESCRIGDLNSAQRYATKAL 181 VQ+AL E+ +A E L+ L+ A +LY++ ++G+L A+ +AL Sbjct: 35 VQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQ--QLGELEKAEDSFRRAL 92 Query: 182 DISPDAPWVTEAVVQQYVLAKEWSRAITFLNQKKKNAKEWNR-NRAILL-----IARSLE 235 ++P+ V+ Y TFL Q+ K + + +AI ARSLE Sbjct: 93 TLNPNNG----DVLNNYG---------TFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLE 139 Query: 236 NA 237 NA Sbjct: 140 NA 141 >gnl|CDD|163109 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose phosphotransferase. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity. Length = 451 Score = 28.3 bits (64), Expect = 5.1 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 18/83 (21%) Query: 1 MLRLIRYFFVISLVICSFIIVSHYPEDVSITWGNRLYRTSPFVILSILYFFLFAWILLFA 60 +LR++ + + L++ + + S W +L +FL A LL Sbjct: 64 LLRILLAWTLTFLILALLAFLLKTGGEFSRLW--------------LLLWFLLALALL-L 108 Query: 61 VSRFFLSCPAMLFHMLHKRNYDK 83 + R L +L L ++ ++ Sbjct: 109 LGRLIL---RLLLRRLRRKGFNL 128 >gnl|CDD|148994 pfam07695, 7TMR-DISM_7TM, 7TM diverse intracellular signalling. This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules). Length = 207 Score = 28.0 bits (63), Expect = 6.5 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 7/67 (10%) Query: 1 MLRLIRYFFVISLVICSFIIVSHYPEDVSITWGNRLYR-TSPFVILSILYFFLFAWILLF 59 + RL+ ++ L++ + Y T RL + + IL +L + AW + Sbjct: 98 LDRLLLGLALLLLLLLLLAPLFPY------TLSLRLAQLLALLFILFLLVLGIIAWRKGY 151 Query: 60 AVSRFFL 66 +R+FL Sbjct: 152 KPARYFL 158 >gnl|CDD|150096 pfam09317, DUF1974, Domain of unknown function (DUF1974). Members of this family of functionally uncharacterized domains are predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases. Length = 284 Score = 27.8 bits (63), Expect = 7.0 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%) Query: 310 KLKRALRLEEINKESVESLVIVSKIALEMGSIDQAHAKAMLAMKIAPRKEI 360 KLK+AL+ ++ K +E L+ + ALE G I + A+ + + A I Sbjct: 232 KLKKALKKGKLPKLRLEELL---EAALEAGVITEEEAELLREAEAARLDAI 279 >gnl|CDD|150299 pfam09586, YfhO, Bacterial membrane protein YfhO. This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family. Length = 835 Score = 27.6 bits (62), Expect = 7.7 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 10/52 (19%) Query: 36 LYRTSPFVILSILYFF----------LFAWILLFAVSRFFLSCPAMLFHMLH 77 +Y ++L ILYFF LFA +LLF + F+L +++H Sbjct: 281 IYVGLLPLLLLILYFFNKLIKLKEKLLFALLLLFLILSFYLPPLDLVWHGFQ 332 >gnl|CDD|181866 PRK09450, cyaA, adenylate cyclase; Provisional. Length = 830 Score = 27.6 bits (62), Expect = 8.4 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 13/61 (21%) Query: 66 LSCPAMLFHMLH-KRNYDKGYKALYTGLMSIAAHNIPLARKMHSYVSQQHTFHNEYLVYL 124 LS P + F + R G+ LY S + Q +N YL L Sbjct: 445 LSEPDLTFIEVPPGRANRSGW-YLYNQAPD-----------PDSIIGHQPLEYNRYLNKL 492 Query: 125 L 125 + Sbjct: 493 V 493 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 0.321 0.134 0.400 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,031,257 Number of extensions: 513145 Number of successful extensions: 1106 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1099 Number of HSP's successfully gapped: 47 Length of query: 492 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 395 Effective length of database: 3,898,497 Effective search space: 1539906315 Effective search space used: 1539906315 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 (21.9 bits) S2: 59 (26.5 bits)