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)