RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780896|ref|YP_003065309.1| ABC transporter membrane
spanning protein (branched chain amino acid) [Candidatus Liberibacter
asiaticus str. psy62]
(351 letters)
>gnl|CDD|183081 PRK11301, livM, leucine/isoleucine/valine transporter permease
subunit; Provisional.
Length = 419
Score = 161 bits (409), Expect = 3e-40
Identities = 107/302 (35%), Positives = 155/302 (51%), Gaps = 22/302 (7%)
Query: 14 ILCLLAVVYPLLLFLFLGATKSQKYIDSMGIQILIYVMFAWGLSIVVGSLGLLSLNCVIA 73
L + AV +P F S+ +D + LIYV+ GL++VVG GLL L V
Sbjct: 95 ALLVAAVAWP-----FFV---SRGAVD-IATLTLIYVILGLGLNVVVGLAGLLDLGYVGF 145
Query: 74 YAIGAYSYVILGSRYGLSIWLLIPVSAMISGACGMIMGLPSLKFRGDYLAIATLIMSEIF 133
YA+GAY+Y +L YGL W +P++ +++ G ++G P L+ RGDYLAI TL EI
Sbjct: 146 YAVGAYTYALLNHYYGLGFWECLPIAGLMAALFGFLLGFPVLRLRGDYLAIVTLGFGEII 205
Query: 134 QNILIKWKPITNGKAGIYVADRLYFLGTTV---------RSLIRFFRFPSSFVIYEIFMY 184
+ +L+ IT G GI + G + FF IF+Y
Sbjct: 206 RILLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFHEFFGLKYDPSDRVIFLY 265
Query: 185 YVLLGMCFLSASIILWLRRTAISNAWRTIRDNQKAFFSL--NTTIIFAKLSAFAVSSAFI 242
V L + L+ +I L R + AW +R+++ A SL N T I KLSAF + +AF
Sbjct: 266 LVALLLVVLTLFVINRLLRMPLGRAWEALREDEIACRSLGLNPTRI--KLSAFTIGAAFA 323
Query: 243 GMAGAFFAASRDRISPDMFKFSENIIVISIVILGGMTSLSKIAKATAILIGVVELCCGMN 302
G AG FFAA + +SP+ F F E+ +++IV+LGGM S + A +L+ + EL N
Sbjct: 324 GFAGTFFAARQGFVSPESFTFIESAFILAIVVLGGMGSQFGVILAAILLVVLPELMRDFN 383
Query: 303 FY 304
Y
Sbjct: 384 EY 385
>gnl|CDD|163439 TIGR03727, urea_t_UrtC_arc, urea ABC transporter, permease protein
UrtC, archaeal type. Members of this protein family are
ABC transporter permease subunits restricted to the
Archaea. Several lines of evidence suggest this protein
is functionally analogous, as well as homologous, to the
UrtC subunit of the Corynebacterium glutamicum urea
transporter. All members of the operon show sequence
similarity to urea transport subunits, the gene is
located near the urease structural subunits in two of
three species, and partial phylogenetic profiling
identifies this permease subunit as closely matching the
profile of urea utilization.
Length = 364
Score = 47.5 bits (113), Expect = 5e-06
Identities = 67/293 (22%), Positives = 105/293 (35%), Gaps = 44/293 (15%)
Query: 17 LLAVVYPLLLFLFLGATKSQKYIDSMGIQILIYVMFAWGLSIVVGSLGLLSLNCVIAYAI 76
L VVYPL+ + S L + LS+V G G+LS V + I
Sbjct: 32 ALLVVYPLIRDSYAAGQFSL---------FLALALLGLSLSVVWGYTGILSFGQVAFFGI 82
Query: 77 GAYSYVILGSRYGLSIWLLIPVSAMISGACGMIMGLPSLKFRGD----YLAIATLIMSEI 132
AY++ ++ +G + + + I L F G Y+ I TL+++ +
Sbjct: 83 AAYTFGVVSINFGTAGGITAALPVAIVVGTISAAILGYFMFYGGVRDVYVTIITLVVTLV 142
Query: 133 FQNILI-----KWKPIT------NGKAGIYVADRLYFLGTTVRSLIRFFRFPSSFVIYEI 181
+ + +W NG I LG S SF E
Sbjct: 143 LETFMAQTAGSEWAIGEAKLGGFNGMPDI----PNLTLGVGGASF--------SFSGSE- 189
Query: 182 FMYYVLLGMCFLSASIILWLRRTAISNAWRT---IRDNQKAFFSLNTTIIFAKLSAFAVS 238
F Y VL + F L LR S + +R++++ + KL F
Sbjct: 190 FYYLVLAVLVF----TYLGLRILVNSKYGYSMVAVREDEERTEMFGYNVKKIKLVVFTFG 245
Query: 239 SAFIGMAGAFFAASRDRISPDMFKFSENIIVISIVILGGMTSLSKIAKATAIL 291
A G++G F+A + I P +F + + V LGG SL AT +
Sbjct: 246 GALAGLSGVFYANWGNYIDPSVFTILFATLPVVWVSLGGRESLLGAIVATVAI 298
>gnl|CDD|132449 TIGR03408, urea_trans_UrtC, urea ABC transporter, permease protein
UrtC. Members of this protein family are ABC
transporter permease proteins associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity.
Length = 313
Score = 45.3 bits (108), Expect = 2e-05
Identities = 52/268 (19%), Positives = 96/268 (35%), Gaps = 48/268 (17%)
Query: 46 ILIYVMFAWGLSIVVGSLGLLSLNCVIAYAIGAYS---YVIL----GSRYGLSI------ 92
L Y + A G+ ++ G G+LSL + + +G Y+ Y+ L GL
Sbjct: 15 YLCYAIVALGIDLIWGYTGILSLGQGVFFGLGGYAMAMYLKLQASGEGTTGLPDFMLWNG 74
Query: 93 -----WLLIPVSAMISGACGMIMGLPSL------------KFRGDYLAIATLIMSEIFQN 135
W P ++ ++ +P L + +G Y +I T ++
Sbjct: 75 VTELPWFWQPFASFPFALL-AVVLVPGLLAFLLGYFVFRSRIKGVYFSIITQALALALAL 133
Query: 136 ILIKWKPITNGKAGIYVADRLYFLGTTVRSLIRFFRFPSSFVIYEIFMYYVLLGMCFLSA 195
+ + + T G G+ F S + +Y++ + L+
Sbjct: 134 LFVGQQTGTGGTNGL-------------TDFKTLLGFDLSSDSTKRALYFLTAALLALAF 180
Query: 196 SIILWLRRTAISNAWRTIRDNQK--AFFSLNTTIIFAKLSAFAVSSAFIGMAGAFFAASR 253
+ WL R+ IRD + F + K+ F +S+ G+AGA +
Sbjct: 181 LLCRWLVRSRFGRVLIAIRDAENRVRFLGYDPANY--KVFVFVLSAGIAGIAGALYVPQV 238
Query: 254 DRISPDMFKFSENIIVISIVILGGMTSL 281
ISP +I ++ V +GG +L
Sbjct: 239 GIISPSEMGIVPSIEMVIWVAVGGRGTL 266
>gnl|CDD|183076 PRK11285, araH, L-arabinose transporter permease protein;
Provisional.
Length = 333
Score = 33.9 bits (78), Expect = 0.073
Identities = 57/230 (24%), Positives = 97/230 (42%), Gaps = 26/230 (11%)
Query: 66 LSLNCVIAYAIGAYSYVILGSRYGLSIWLLIPVSAMISGACGMIMGLPSLKFRGDYLAIA 125
LS+ V+A+A + VI + S+WL + ++ A G++ G + + + L I
Sbjct: 84 LSVASVVAFAGVVTAVVINATE---SLWLGVAAGLLLGAAVGLVNGFVIARLKINAL-IT 139
Query: 126 TLIMSEIFQNI-LIKWKPITNGKAGIYVADRLYFLGTTVRSLIRFFRFPSSFVIYEIFMY 184
TL +I + + I I++GKA +R + LG FF P+ I+
Sbjct: 140 TLATMQIVRGLAYI----ISDGKAVGISDERFFALGYA-----NFFGVPAP--IWLTVAC 188
Query: 185 YVLLGMCFLSASIILWLRRTAISNAWRTIRDNQKAFFSLNTTIIFAKLSAFAVSSAFIGM 244
+V+ G L +T I N++A ++ K+ F + +
Sbjct: 189 FVVFG---------FLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLQGLVSAL 239
Query: 245 AGAFFAASRDRISPDMFKFSENIIVISIVILGGMTSLSKIAKATAILIGV 294
AG A SR M +IVIS +LGG++ IAK + ++ GV
Sbjct: 240 AGVILA-SRMTSGQPMTSIGFELIVISACVLGGVSLKGGIAKISGVVAGV 288
>gnl|CDD|132450 TIGR03409, urea_trans_UrtB, urea ABC transporter, permease protein
UrtB. Members of this protein family are ABC
transporter permease proteins associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity.
Length = 291
Score = 30.3 bits (69), Expect = 0.75
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 48 IYVMFAWGLSIVVGSLGLLSLNCVIAYAIGAYSYVILGS------RYGLSIWLLIPVSAM 101
I ++ A GL+I G +G++++ IGAY+ ++ L + + IP++ +
Sbjct: 13 ILLLAALGLAITFGQMGVINMAHGEFIMIGAYTTYVVQQLFSAPGLADLYLLIAIPLAFL 72
Query: 102 ISGACGMIM 110
+S G ++
Sbjct: 73 VSALLGALI 81
>gnl|CDD|130830 TIGR01769, GGGP, geranylgeranylglyceryl phosphate synthase. This
model represents geranylgeranylglyceryl phosphate
synthase which catalyzes the first committed step in the
synthesis of ether-linked membrane lipids in archaea.
The active enzyme is reported to be a homopentamer in
Methanobacterium thermoautotrophicum but is reported to
be a homodimer in Thermoplasma acidophilum.
Length = 205
Score = 30.1 bits (68), Expect = 0.93
Identities = 23/118 (19%), Positives = 45/118 (38%), Gaps = 10/118 (8%)
Query: 185 YVLLGMCFLSASIILWLRRTAISNAWRTIRDNQKAFFSLNTTII----FAKLSAFAVSSA 240
Y ++G L A IL L I A+ + + I +A+ +++
Sbjct: 85 YFIVGAQILGAITILKLNLEVIPMAYLIVGPGGAVGYVGKAREIPYNKPEIAAAYCLAAK 144
Query: 241 FIGMAGAFFAA---SRDRISPDMFKFSENIIVISIVILGGMTSLS---KIAKATAILI 292
+ GM + A + ++P+ + I +++ GG+ S +I A A I
Sbjct: 145 YFGMKWVYLEAGSGASYPVNPETISLVKKASGIPLIVGGGIRSPEIAYEIVLAGADAI 202
>gnl|CDD|152276 pfam11840, DUF3360, Protein of unknown function (DUF3360). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 489 to 517 amino acids in
length.
Length = 491
Score = 29.7 bits (67), Expect = 1.1
Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 20/111 (18%)
Query: 15 LCLLAVVYPLLLFLFLGATKSQK------------YIDSMGIQILIYVMFAWGLSIVVGS 62
L +L V+ L+L LF G +K Y+ +G I +FAW +G
Sbjct: 146 LGILIGVFGLILSLFKGGSKLVNLTSEGVCGGLLIYLGFIGTTSQIKKLFAWAGGFGMGY 205
Query: 63 LGLLSLNCVIAYAIGAYSYVILGSRYGLSIWLLIPVSAMISGACGMIMGLP 113
+ + VI I Y+Y+ ++ WL IP+ ++++G MG P
Sbjct: 206 IAFV----VILVTIVIYAYL---AKIRKR-WLAIPLCSLLAGVVAFAMGAP 248
>gnl|CDD|163581 TIGR03869, F420-0_ABCperm, proposed F420-0 ABC transporter,
permease protein. his small clade of ABC-type
transporter permease protein components is found as a
three gene cassette along with a periplasmic
substrate-binding protein (TIGR03868) and an ATPase
(TIGR03873). The organisms containing this cassette are
all Actinobacteria and all contain numerous genes
requiring the coenzyme F420. This model was defined
based on five such organisms, four of which are lacking
all F420 biosynthetic capability save the final
side-chain polyglutamate attachment step (via the gene
cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and
marine actinobacterium PHSC20C1 this cassette is in an
apparent operon with the cofE gene and, in PHSC20C1,
also with an F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this permease protein is a component of
a F420-0 (that is, F420 lacking only the polyglutamate
tail) transporter.
Length = 325
Score = 28.7 bits (64), Expect = 2.4
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 50 VMFAWGLSIVVGSLGLLSLNCVIAYAIGAYSYVILGSRYGLSIWLLIPVSAMISGACGMI 109
V A G +VVG + L S + A+A G S LG + WLL+ + A+++GA +
Sbjct: 187 VAIAGGALLVVGLVLLASGRVLDAFAFGDSSAAALGVDVERTRWLLLTLVALLTGALVSV 246
Query: 110 MG 111
G
Sbjct: 247 SG 248
>gnl|CDD|177761 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 28.4 bits (64), Expect = 3.0
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 14/36 (38%)
Query: 164 RSLIRF--------------FRFPSSFVIYEIFMYY 185
R+LIR FR +F +Y FM+
Sbjct: 548 RALIRLCSKFGDYRKDDPSSFRLSPNFSLYPQFMFN 583
>gnl|CDD|179759 PRK04164, PRK04164, hypothetical protein; Provisional.
Length = 181
Score = 27.9 bits (63), Expect = 4.0
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 14 ILCLLAVVY-PLLLFLFLGATKSQKYIDS-MG-IQILIYVMFAWGLSIVVGSLGLLSLNC 70
++ ++ ++Y +L + K +Y+ + +G +++LIYV+ L +V +L +
Sbjct: 12 LIFIIRIIYVSILTIRTILTVKGYRYLAALLGFLEVLIYVV---ALGLVFQNLD--NPQN 66
Query: 71 VIAYAIGAYSYVILGSR 87
+IAYA+G + +G +
Sbjct: 67 IIAYALGFAVGIYVGMK 83
>gnl|CDD|173241 PRK14780, PRK14780, lipoprotein signal peptidase; Provisional.
Length = 263
Score = 27.6 bits (61), Expect = 5.2
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 129 MSEIFQNILIKWKPITNGKAGIYVADRLYFLGTTVRSLIRFFRFPSSFVIYEIFMYYVLL 188
+ IF N LI + G I ++ +++F +S I +F Y+++
Sbjct: 165 LPGIFHNSLINPNSVGGGDDVI-------------NGVVDYWKFVNS--IINLFDVYIVV 209
Query: 189 GMCFLSASIIL 199
G+C L +I+
Sbjct: 210 GVCVLVVILII 220
>gnl|CDD|132661 TIGR03622, urea_t_UrtB_arc, urea ABC transporter, permease protein
UrtB. Members of this protein family are ABC
transporter permease subunits restricted to the Archaea.
Several lines of evidence suggest this protein is
functionally analogous, as well as homologous, to the
UrtB subunit of the Corynebacterium glutamicum urea
transporter. All members of the operon show sequence
similarity to urea transport subunits, the gene is
located near the urease structural subunits in two of
three species, and partial phylogenetic profiling
identifies this permease subunit as closely matching the
profile of urea utilization.
Length = 283
Score = 27.5 bits (61), Expect = 5.8
Identities = 49/216 (22%), Positives = 93/216 (43%), Gaps = 25/216 (11%)
Query: 50 VMFAWGLSIVVGSLGLLSLNCVIAYAIGAYSYVILGSRYGLSIWLLIPVSAMISGACGMI 109
V+ A GL+++ G +G+++L +GAY + + GL + AM+SG +
Sbjct: 15 VLAAVGLAVIFGMMGVINLAHGEFILVGAYGTTLTYHQAGLPL-----PVAMVSGVVMTV 69
Query: 110 MGLPSLKFRGDYLAIATLIMSEIFQNILIKWKPITNGKAGIYVADRLYFLGTTVRSLIRF 169
+ + I ++ + + L+ T G A I G ++ S+
Sbjct: 70 I----------FGIIVERLIIQHLYDRLLDSMVATFGLALILTQGLRITFGNSLDSISTP 119
Query: 170 F----RFPSSFVIYEIFMYYVLLGMCFLSASIILWLRRTAISNAWRTIRDNQKA-FFSLN 224
F P ++ Y +F+ V +G+ L +L+ R A TI+D + A ++
Sbjct: 120 FGNVAYGPYTYSTYRVFLPLVAIGV--LVGLYVLFTRTEFGVRARATIQDPETARAMGVD 177
Query: 225 TTIIFAKLSAFAVSSAFIGMAGAFFAASRDRISPDM 260
T ++ ++ FA+ S G+ GA +A I+PD
Sbjct: 178 TDRMY--VTTFAIGSGLAGLTGALYAPI-GAITPDR 210
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
0.333 0.144 0.433
Gapped
Lambda K H
0.267 0.0619 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,715,774
Number of extensions: 378479
Number of successful extensions: 1625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1613
Number of HSP's successfully gapped: 73
Length of query: 351
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 257
Effective length of database: 3,963,321
Effective search space: 1018573497
Effective search space used: 1018573497
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 58 (26.4 bits)