RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780308|ref|YP_003064721.1| putative membrane-bound lytic murein transglycosylase signal peptide protein [Candidatus Liberibacter asiaticus str. psy62] (288 letters) >gnl|CDD|162796 TIGR02283, MltB_2, lytic murein transglycosylase. Members of this family are closely related to the MltB family lytic murein transglycosylases described by TIGR02282 and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many members of this family (unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (pfam01471), not included in region described by this model. Many sequences appear to contain N-terminal lipoprotein attachment sites, as does E. coli MltB in TIGR02282. Length = 300 Score = 199 bits (507), Expect = 1e-51 Identities = 78/205 (38%), Positives = 117/205 (57%), Gaps = 9/205 (4%) Query: 42 FGEWKSAARARAVREGMSPKTAKHLFADLEYLD-TTIARDRKMVTSPPV---SFKDYLDG 97 F W + RA A +G+S T FA ++ D + + DR + P +F DYL Sbjct: 2 FDAWLAQLRAEAAAKGISAATFDRAFAGIKEPDQSVLNLDR----NQPEFTQTFWDYLSR 57 Query: 98 LSSSEIIAQGIALKKANSRLLINLKKEYGVPPGILMALWGLETHFGETMGKTPLLSTLAT 157 S IA G A+ + + LL ++K YGVP IL+A+WG+E+ FG GK ++ +LAT Sbjct: 58 RVSPRRIAIGRAMLQRYAALLARIEKRYGVPAEILLAIWGMESDFGAYQGKFDVIRSLAT 117 Query: 158 LAYDCRRAKFFTEQFFYALDLVKKGVISSHAL-GATFGEIGQFQFLPVNVVKYAIDADED 216 LAYD RR +F + AL ++++G ++ A+ G+ G +GQ QFLP + + YA+D D D Sbjct: 118 LAYDGRRKDYFRTELIAALKILQRGDLTRAAMKGSWAGAMGQTQFLPSSYLNYAVDFDGD 177 Query: 217 GKIDLVKSNIDAIASAAKFLAKLGW 241 G+ D+ S DA+AS A +L GW Sbjct: 178 GRRDIWNSVPDALASTANYLVNGGW 202 Score = 39.3 bits (92), Expect = 0.001 Identities = 12/28 (42%), Positives = 15/28 (53%) Query: 252 KNFAILKHWNASLNYNKTIAYIAAHIDG 279 NF ++K WN S Y TI +A I G Sbjct: 273 PNFRVIKEWNRSDYYALTIGLLADRIAG 300 >gnl|CDD|162795 TIGR02282, MltB, lytic murein transglycosylase B. This family consists of lytic murein transglycosylases (murein hydrolases) in the family of MltB, which is a membrane-bound lipoprotein in Escherichia coli. The N-terminal lipoprotein modification motif is conserved in about half the members of this family. The term Slt35 describes a naturally occurring soluble fragment of MltB. Members of this family never contain the putative peptidoglycan binding domain described by Pfam model pfam01471, which is associated with several classes of bacterial cell wall lytic enzymes. Length = 290 Score = 114 bits (288), Expect = 2e-26 Identities = 63/188 (33%), Positives = 95/188 (50%), Gaps = 19/188 (10%) Query: 66 LFADLEYLDTTIARDRKMVTSPPVSFK---DYLDGLSSSEIIAQGIALKKANSRLLINLK 122 + A +Y D I +++ +P S K +Y + + I G+ K + L + Sbjct: 21 ILAQAKYNDEVI----RLIDNPAESAKPWLEYRGIFITPKRIQDGVEFWKQHEDALNRAE 76 Query: 123 KEYGVPPGILMALWGLETHFGETMGKTPLLSTLATLAYDC-RRAKFFTEQFFYALDLVK- 180 + YGVPP I++A+ G+ET++G MGK +L L TLA+D RRA FF + L L + Sbjct: 77 QRYGVPPEIIVAIIGVETNYGRNMGKYRVLDALTTLAFDYPRRATFFRGELGQFLLLARE 136 Query: 181 -----KGVISSHALGATFGEIGQFQFLPVNVVKYAIDADEDGKIDLVKSNIDAIASAAKF 235 + S+A G +G QF+P + +YA+D D DG IDL S DAI S A + Sbjct: 137 EQLDPLTLKGSYA-----GAMGYPQFMPSSYRQYAVDFDGDGHIDLWNSPDDAIGSVANY 191 Query: 236 LAKLGWTK 243 GW + Sbjct: 192 FHAHGWVR 199 >gnl|CDD|182706 PRK10760, PRK10760, murein hydrolase B; Provisional. Length = 359 Score = 93.3 bits (232), Expect = 6e-20 Identities = 46/123 (37%), Positives = 72/123 (58%), Gaps = 3/123 (2%) Query: 123 KEYGVPPGILMALWGLETHFGETMGKTPLLSTLATLAYDC-RRAKFFTEQFFYALDLVKK 181 + YGVPP I++ + G+ET +G MGKT +L LATL+++ RRA++F+ + L + + Sbjct: 144 QVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARD 203 Query: 182 GVISSHALGATF-GEIGQFQFLPVNVVKYAIDADEDGKIDLVKSNIDAIASAAKFLAKLG 240 L +F G +G QF+P + +YA+D + DG I+L +DAI S A + G Sbjct: 204 EGDDPLNLRGSFAGAMGYGQFMPSSFKQYAVDFNGDGHINLWDP-VDAIGSVANYFKAHG 262 Query: 241 WTK 243 W K Sbjct: 263 WVK 265 >gnl|CDD|182561 PRK10575, PRK10575, iron-hydroxamate transporter ATP-binding subunit; Provisional. Length = 265 Score = 32.1 bits (73), Expect = 0.18 Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 3/40 (7%) Query: 93 DYLDGLSSSEIIAQGIALKKANSRLLINLKKEYGVPPGIL 132 DYL L E+IAQG + L + YG+P GIL Sbjct: 216 DYLVALRGGEMIAQGTPAELMRGETLEQI---YGIPMGIL 252 >gnl|CDD|182660 PRK10701, PRK10701, DNA-binding transcriptional regulator RstA; Provisional. Length = 240 Score = 31.1 bits (71), Expect = 0.29 Identities = 12/27 (44%), Positives = 16/27 (59%) Query: 135 LWGLETHFGETMGKTPLLSTLATLAYD 161 LW L TH G+ M + LL L ++YD Sbjct: 170 LWELATHAGQIMDRDALLKNLRGVSYD 196 >gnl|CDD|162188 TIGR01070, mutS1, DNA mismatch repair protein MutS. Length = 840 Score = 27.4 bits (61), Expect = 3.9 Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 1/70 (1%) Query: 90 SFKDYLDGLSSSEIIAQGIALKKANSRLLINLKKEYGVPPGILMALWGLE-THFGETMGK 148 + L + E +A +AL A R L L+ P + L LE + Sbjct: 322 GLRPLLKEVGDLERLAARVALGNARPRDLARLRTSLEQLPELRALLEELEGPTLQALAAQ 381 Query: 149 TPLLSTLATL 158 S L L Sbjct: 382 IDDFSELLEL 391 >gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional. Length = 203 Score = 27.4 bits (61), Expect = 4.8 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 9/51 (17%) Query: 57 GMSPKTAKHLFADLEYLDTTIARDRKMVTSPPVS-------FKDYLDGLSS 100 G+ KTA+H+F +L+Y + F+D L GL++ Sbjct: 116 GIGKKTAQHIFLELKY--KLKVEGLPAAAVLAGTGAVPGSVFRDALAGLAN 164 >gnl|CDD|163338 TIGR03588, PseC, UDP-4-keto-6-deoxy-N-acetylglucosamine 4-aminotransferase. This family of enzymes are aminotransferases of the pfam01041 family involved in the biosynthesis of pseudaminic acid. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species. Length = 380 Score = 26.5 bits (59), Expect = 7.7 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 17/69 (24%) Query: 185 SSHALGATFG----------EIGQFQFLPVNVVKYAIDADEDGKIDLVKSNIDAIASAAK 234 +SHALGA +G + F F PV ++ A E G V +N + +A + Sbjct: 155 ASHALGAEYGGKPVGNCRYADATVFSFHPVKIITTA----EGG---AVTTNDEELAERMR 207 Query: 235 FLAKLGWTK 243 L G TK Sbjct: 208 LLRSHGITK 216 >gnl|CDD|131352 TIGR02299, HpaE, 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase. This model represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring. Length = 488 Score = 26.7 bits (59), Expect = 8.0 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 4/32 (12%) Query: 118 LINLKKEYGVPPGILMALWGLETHFGETMGKT 149 L + KE G+P G+ + G FGE GK Sbjct: 181 LAEIAKEAGLPDGVFNLVHG----FGEEAGKA 208 >gnl|CDD|161755 TIGR00193, urease_gam, urease, gamma subunit. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species. Length = 102 Score = 26.4 bits (58), Expect = 8.7 Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%) Query: 264 LNYNKTIAYIAAHI-DGVPIGKG 285 LNY + +AYI+AHI +G GK Sbjct: 30 LNYPEAVAYISAHIMEGARDGKK 52 >gnl|CDD|149573 pfam08571, Yos1, Yos1-like. In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes. Length = 77 Score = 26.4 bits (59), Expect = 9.2 Identities = 10/26 (38%), Positives = 16/26 (61%) Query: 228 AIASAAKFLAKLGWTKCAGYQPGEKN 253 AI S +FL+++GW+ A G +N Sbjct: 16 AILSEDRFLSRIGWSSSAASGNGSEN 41 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 0.135 0.399 Gapped Lambda K H 0.267 0.0721 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,722,109 Number of extensions: 299154 Number of successful extensions: 637 Number of sequences better than 10.0: 1 Number of HSP's gapped: 632 Number of HSP's successfully gapped: 16 Length of query: 288 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 196 Effective length of database: 4,006,537 Effective search space: 785281252 Effective search space used: 785281252 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: 57 (25.8 bits)