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)