RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781174|ref|YP_003065587.1| outer membrane assembly lipoprotein YfiO [Candidatus Liberibacter asiaticus str. psy62] (271 letters) >gnl|CDD|163209 TIGR03302, OM_YfiO, outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). Length = 235 Score = 192 bits (490), Expect = 8e-50 Identities = 83/238 (34%), Positives = 125/238 (52%), Gaps = 3/238 (1%) Query: 22 FALTIFFSIAVCFLVGWERQSSRDVYLDSVTDVRYQREVYEKAVLFLKEQNFSKAYEYFN 81 L I + L G S + D V + E+YE+A L ++++A +YF Sbjct: 1 LLLLILLLALLLLLAGC--SSKKKKEADPVEE-WPAEELYEEAKEALDSGDYTEAIKYFE 57 Query: 82 QCSRDFPFAGVARKSLLMSAFVQYSAGKYQQAASLGEEYITQYPESKNVDYVYYLVGMSY 141 +PF+ A ++ L A+ Y +G Y +A + + +I +P + DY YYL G+S Sbjct: 58 ALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSN 117 Query: 142 AQMIRDVPYDQRATKLMLQYMSRIVERYTNSPYVKGARFYVTVGRNQLAAKEVEIGRYYL 201 I V DQ A + + ++ RY NS Y A+ + RN+LA KE+ + R+YL Sbjct: 118 YNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYL 177 Query: 202 KRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYVALALMDEAREVVSLIQERYPQ 259 KRG YVAAI RF+ V+ NY D EEA+ARLVEAY+ L L D A++ +++ YP Sbjct: 178 KRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYPD 235 >gnl|CDD|182792 PRK10866, PRK10866, outer membrane biogenesis protein BamD; Provisional. Length = 243 Score = 68.6 bits (168), Expect = 2e-12 Identities = 51/206 (24%), Positives = 91/206 (44%), Gaps = 12/206 (5%) Query: 59 EVYEKAVLFLKEQNFSKAYEYFNQCSRDFPFAGVARKSLLMSAFVQYSAGKYQQAASLGE 118 E+Y A L++ N+ +A +PF +++ L + Y A + + Sbjct: 34 EIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAID 93 Query: 119 EYITQYPESKNVDYVYYLVGMSYAQMIRDVPY-----------DQRATKLMLQYMSRIVE 167 +I P N+DYV Y+ G++ + D D + + + S++V Sbjct: 94 RFIRLNPTHPNIDYVLYMRGLT-NMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVR 152 Query: 168 RYTNSPYVKGARFYVTVGRNQLAAKEVEIGRYYLKRGEYVAAIPRFQLVLANYSDAEHAE 227 Y NS Y A + +++LA E+ + YY KRG YVA + R + +L +Y D + Sbjct: 153 GYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATR 212 Query: 228 EAMARLVEAYVALALMDEAREVVSLI 253 +A+ + AY L L +A +V +I Sbjct: 213 DALPLMENAYRQLQLNAQADKVAKII 238 >gnl|CDD|131842 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction. Length = 119 Score = 43.0 bits (102), Expect = 7e-05 Identities = 20/94 (21%), Positives = 40/94 (42%), Gaps = 14/94 (14%) Query: 166 VERYTNSPYVKGARFYVTVGRNQLAAKEVEIGRYYLKRGEYVAAIPRFQLVLANYSDAEH 225 +++Y S Y A ++ +G Y +G+Y A F V+ Y + Sbjct: 29 LKKYPKSTYAPNAHYW--------------LGEAYYAQGKYADAAKAFLAVVKKYPKSPK 74 Query: 226 AEEAMARLVEAYVALALMDEAREVVSLIQERYPQ 259 A +A+ +L + L ++A+ + + +RYP Sbjct: 75 APDALLKLGMSLQELGDKEKAKATLQQVIKRYPG 108 Score = 30.7 bits (70), Expect = 0.37 Identities = 28/126 (22%), Positives = 52/126 (41%), Gaps = 14/126 (11%) Query: 57 QREVYEKAVLFLKEQNFSKAYEYFNQCSRDFP---FAGVARKSLLMSAFVQYSAGKYQQA 113 + Y+ A+L LK +++ A + F + +P +A A L Y+ GKY A Sbjct: 2 EEAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWL---GEAYYAQGKYADA 58 Query: 114 ASLGEEYITQYPESKNVDYVYYLVGMSYAQMIRDVPYDQRATKLMLQYMSRIVERYTNSP 173 A + +YP+S +GMS ++ + + ++++RY S Sbjct: 59 AKAFLAVVKKYPKSPKAPDALLKLGMSLQEL--------GDKEKAKATLQQVIKRYPGSS 110 Query: 174 YVKGAR 179 K A+ Sbjct: 111 AAKLAQ 116 Score = 28.8 bits (65), Expect = 1.4 Identities = 21/64 (32%), Positives = 30/64 (46%) Query: 200 YLKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYVALALMDEAREVVSLIQERYPQ 259 LK G+Y AI FQ L Y + +A A L EAY A +A + + ++YP+ Sbjct: 12 VLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPK 71 Query: 260 GYWA 263 A Sbjct: 72 SPKA 75 >gnl|CDD|183314 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional. Length = 389 Score = 39.4 bits (93), Expect = 0.001 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 2/62 (3%) Query: 197 GRYYLKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYVALALMDEAREVVSLIQER 256 G L +G+Y AAI + V D E+ E + +L+E Y AL E E + E Sbjct: 221 GDLALAQGDYAAAIEALERVE--EQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE 278 Query: 257 YP 258 YP Sbjct: 279 YP 280 >gnl|CDD|183248 PRK11636, mrcA, penicillin-binding protein 1a; Provisional. Length = 850 Score = 31.3 bits (71), Expect = 0.26 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 14/82 (17%) Query: 116 LGEEYIT--QYPESKNVDYVYYLVGMSYA-QMIRDVPYDQRATKLMLQYMSRIVERYTNS 172 L E YIT QY ++++ +V +A ++ PY ++++ Q M RY + Sbjct: 230 LDEGYITQAQYDQARSEP----IVANYHAPEIAFSAPY---LSEMVRQEM---YNRYGEN 279 Query: 173 PYVKGARFYVTVGR-NQLAAKE 193 Y G R Y T+ R Q AA++ Sbjct: 280 AYEDGYRVYTTITRKVQQAAQQ 301 >gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. Length = 423 Score = 30.0 bits (68), Expect = 0.74 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 5/76 (6%) Query: 187 NQLAAKEVEIGRYYLKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYVALALMDE- 245 + A + E+GR + I QL + EE + L EA LA + E Sbjct: 203 RERAEAQGELGRLEAELEVLKRQIDELQLERQQI-EQTFREEVLEELTEAQARLAELRER 261 Query: 246 ---AREVVSLIQERYP 258 AR+ + + R P Sbjct: 262 LNKARDRLQRLIIRSP 277 >gnl|CDD|148262 pfam06552, TOM20_plant, Plant specific mitochondrial import receptor subunit TOM20. This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesized in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria. Length = 186 Score = 29.2 bits (65), Expect = 1.3 Identities = 17/64 (26%), Positives = 23/64 (35%), Gaps = 6/64 (9%) Query: 72 NFSKAYEYFNQCSRDFPFAGVARKSLLMSA------FVQYSAGKYQQAASLGEEYITQYP 125 NF KA ++F Q + P + RKSL M+A + G QQ Sbjct: 95 NFDKATQFFQQAVDEQPDNDLYRKSLEMAAKAPELHMEFHKQGLGQQIMGGEASSSPSTK 154 Query: 126 ESKN 129 K Sbjct: 155 TVKK 158 >gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional. Length = 1157 Score = 28.5 bits (64), Expect = 1.7 Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 3/48 (6%) Query: 201 LKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYVALALMDEARE 248 +RG+Y AA +Q VL + +A +A L+E +A + AR Sbjct: 614 QQRGDYAAARAAYQRVLTR--EPGNA-DARLGLIEVDIAQGDLAAARA 658 >gnl|CDD|169751 PRK09260, PRK09260, 3-hydroxybutyryl-CoA dehydrogenase; Validated. Length = 288 Score = 28.6 bits (64), Expect = 1.9 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%) Query: 206 YVAAIPRFQLVLANYSDA--EHAEEAMARLVEAYVALALMDEA 246 YV A+ FQ L + E A++ +A + E VA + EA Sbjct: 18 YVFAVSGFQTTLVDIKQEQLESAQQEIASIFEQGVARGKLTEA 60 >gnl|CDD|185626 PTZ00447, PTZ00447, apical membrane antigen 1-like protein; Provisional. Length = 508 Score = 28.4 bits (63), Expect = 2.1 Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 1/61 (1%) Query: 1 MSAVLGRAICIFEAWAYQL-YKFALTIFFSIAVCFLVGWERQSSRDVYLDSVTDVRYQRE 59 +S VL + IC+F+ +AY Y A I +CFL + + + ++++ + R+ Sbjct: 241 ISFVLEQEICVFDFYAYVPKYMSAKEIMGEWFLCFLCFKDGKEQDVINIETIIERNIHRD 300 Query: 60 V 60 + Sbjct: 301 I 301 >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 = 27.7 bits (62), Expect = 3.3 Identities = 42/229 (18%), Positives = 74/229 (32%), Gaps = 60/229 (26%) Query: 54 VRYQREVYEKAVLFLKEQNFSKAYEYFNQCSRDFPFAGVARKSLLMSAFVQYSAGKYQQA 113 V +Q++ YE A L + A EY +LL++ +Y G +QA Sbjct: 270 VDFQKKNYEDARETL-QDALKSAPEYLP--------------ALLLAGASEYQLGNLEQA 314 Query: 114 ASLGEEYITQYPESKNVDYVYYLVGMSYAQMIRDVPYDQRATKLMLQYMSRIVERYTNSP 173 + + P S L+ ++ R D+ L S + + P Sbjct: 315 YQYLNQILKYAPNS---HQARRLLASIQLRLGR---VDEAIATL-----SPALGLDPDDP 363 Query: 174 ---------------YVKGARFYVTVGRN--QLAAKEVEIGRYYLKRGEYVAAIPRFQLV 216 + K A + + AA ++G L +G+ AI Sbjct: 364 AALSLLGEAYLALGDFEKAAEYLAKATELDPENAAARTQLGISKLSQGDPSEAI------ 417 Query: 217 LANYSDAEHAEEAMARLVEAYVALAL-------MDEAREVVSLIQERYP 258 +D E A + L A + L L D+A ++++ P Sbjct: 418 ----ADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAKKLEKKQP 462 >gnl|CDD|180016 PRK05325, PRK05325, hypothetical protein; Provisional. Length = 401 Score = 27.5 bits (62), Expect = 3.4 Identities = 10/28 (35%), Positives = 12/28 (42%), Gaps = 6/28 (21%) Query: 239 ALALMDEAREVVSLIQERYPQGYWARYV 266 A L E +I+ERYP W Y Sbjct: 294 AYKLALE------IIEERYPPAEWNIYA 315 >gnl|CDD|180897 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional. Length = 251 Score = 27.1 bits (61), Expect = 4.9 Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 14/63 (22%) Query: 177 GARFYVTVGRNQLAAKEV--EIGRYYLKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLV 234 GAR VT RN+ AA+ V EI G A+ A+ SD E A+A + Sbjct: 29 GARVVVT-DRNEEAAERVAAEILA-----GGRAIAVA------ADVSDEADVEAAVAAAL 76 Query: 235 EAY 237 E + Sbjct: 77 ERF 79 >gnl|CDD|183379 PRK11915, PRK11915, glycerol-3-phosphate acyltransferase; Reviewed. Length = 621 Score = 26.8 bits (59), Expect = 5.4 Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 4/74 (5%) Query: 179 RFYVTVGRNQLAAKEVEIGRYYLKRGEYVAAIPRFQLVLANYSDAEHAEEAMARLVEAYV 238 RF V + R Q +GR YL GE + R Q + A+ S E +A VE + Sbjct: 267 RFLVRLARQQ----GERLGRAYLDFGEPLPLRKRLQELRADKSGTGSEIERIALDVEHRI 322 Query: 239 ALALMDEAREVVSL 252 A VVSL Sbjct: 323 NRATPVTPTAVVSL 336 >gnl|CDD|150832 pfam10220, DUF2146, Uncharacterized conserved protein (DUF2146). This is a family of proteins conserved from plants to humans. In Dictyostelium it is annotated as Mss11p but this could not be confirmed. Mss11p is required for the activation of pseudo-hyphal and invasive growth by Ste12p in yeast. Length = 890 Score = 26.7 bits (59), Expect = 7.3 Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 1/42 (2%) Query: 11 IFEAWAYQLYKFALTIFFSIAVC-FLVGWERQSSRDVYLDSV 51 E W +F + F +VC LV E S+ D+ + Sbjct: 95 AHEFWKGIECQFCRMLLFLFSVCHILVLVEPTSTFDLSYIRL 136 >gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization protein TraN; Provisional. Length = 1062 Score = 26.6 bits (58), Expect = 7.7 Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 2/39 (5%) Query: 68 LKEQNFSKAYEYFNQCSRDFPFAGVARK--SLLMSAFVQ 104 LK+ KAYE RDF F VA ++ SA VQ Sbjct: 808 LKQMAMKKAYELLPDTVRDFVFKNVATTGGEVVFSAAVQ 846 >gnl|CDD|183824 PRK12902, secA, preprotein translocase subunit SecA; Reviewed. Length = 939 Score = 26.6 bits (59), Expect = 8.0 Identities = 12/40 (30%), Positives = 18/40 (45%) Query: 93 ARKSLLMSAFVQYSAGKYQQAASLGEEYITQYPESKNVDY 132 AR L++S V+ KYQ+AA + + DY Sbjct: 222 ARTPLIISGQVERPQEKYQKAAEVAAALQRKDGIDPEGDY 261 >gnl|CDD|151157 pfam10643, Cytochrome-c551, Photosystem P840 reaction-centre cytochrome c-551. A photosynthetic reaction-centre complex is found in certain green sulphur bacteria such as Chlorobium vibrioforme which are anaerobic photo-auto-trophic organisms. The primary electron donor is P840, a probable B-Chl a dimer, and the primary electron acceptor is a B-Chl monomer. Also on the donor side c-type cytochromes are known to function as electron donors to photo-oxidized P840. This family is thus the secondary endogenous donor of the photosynthetic reaction-centre complex and is a membrane-bound cytochrome containing a single haem group. Length = 213 Score = 26.0 bits (57), Expect = 9.9 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 22 FALTIFFSIAVCFLVGWERQS 42 F L+IF +AV F WER S Sbjct: 82 FPLSIFVIVAVMFASLWERPS 102 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 0.324 0.135 0.393 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: 4,473,388 Number of extensions: 285294 Number of successful extensions: 899 Number of sequences better than 10.0: 1 Number of HSP's gapped: 888 Number of HSP's successfully gapped: 37 Length of query: 271 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 179 Effective length of database: 4,006,537 Effective search space: 717170123 Effective search space used: 717170123 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.4 bits)