RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780561|ref|YP_003064974.1| thiamine transporter substrate
binding subunit [Candidatus Liberibacter asiaticus str. psy62]
(338 letters)
>gnl|CDD|183039 PRK11205, tbpA, thiamine transporter substrate binding subunit;
Provisional.
Length = 330
Score = 526 bits (1358), Expect = e-150
Identities = 184/310 (59%), Positives = 241/310 (77%)
Query: 28 AKPVLTVYTYNSFVADEGAGPKIKQAFERKCNCELKLIGLSDGVALLNKLRMEGENSAAD 87
AKPVLTVYTY+SF A+ G GP +K+AFE +C CELK + L DGV+LLN+LR+EG+NS AD
Sbjct: 21 AKPVLTVYTYDSFAAEWGPGPAVKKAFEAECGCELKFVALEDGVSLLNRLRLEGKNSKAD 80
Query: 88 IVLGFDNNLIDLARKTGLFAKSNIDASQLKLPIKWDDDIFVPYDYGYLAFIYDKRQITQP 147
+VLG DNNL+ A++TGLFA S +D S + +P W+DD FVPYDYGY AF+YDK ++ P
Sbjct: 81 VVLGLDNNLLAAAKQTGLFAPSGVDTSAVTVPGGWNDDTFVPYDYGYFAFVYDKEKLKNP 140
Query: 148 PKNFDELINSTKPWKIIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGW 207
PK+ EL+ S + WK+IYQDPRTST GLGLLLW++K+YGD++ Q W+K+A KT TVTKGW
Sbjct: 141 PKSLKELVESDQNWKVIYQDPRTSTPGLGLLLWMKKVYGDDAPQAWQKLAKKTVTVTKGW 200
Query: 208 TESYGFFLKGESDFVLSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQ 267
+E+YG FLKGE+D VLSY+TSP ++++ +D+Y AA FSEGHYLQ+EVAA+ SKQP+
Sbjct: 201 SEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVEVAARTAASKQPE 260
Query: 268 LAQEFMQFMISPSFQRILPTTNWMYPVVDISMPDVYQAIRIPQKSLRFNAEETTRYRNQW 327
LAQ+F+QFM+SP+FQ +PT NWMYPV +++P ++ + P +L F EE R W
Sbjct: 261 LAQKFLQFMVSPAFQNAIPTGNWMYPVAKVTLPAGFETLTKPATTLLFTPEEVAAQRKAW 320
Query: 328 ISSWQNAVSR 337
IS WQ AVSR
Sbjct: 321 ISEWQRAVSR 330
>gnl|CDD|130343 TIGR01276, thiB, thiamine ABC transporter, periplasmic binding
protein. This model finds the thiamine (and thiamine
pyrophosphate) ABC transporter periplasmic binding
protein ThiB in proteobacteria. Completed genomes having
this protein (E. coli, Vibrio cholera, Haemophilus
influenzae) also have the permease ThiP, described by
TIGRFAMs equivalog model TIGR01253.
Length = 309
Score = 425 bits (1094), Expect = e-120
Identities = 185/309 (59%), Positives = 241/309 (77%)
Query: 29 KPVLTVYTYNSFVADEGAGPKIKQAFERKCNCELKLIGLSDGVALLNKLRMEGENSAADI 88
KPVLTVYTY+SF AD G GP +K+AFE CNCELKL+ L DGV+LLN+LR+EG+NS AD+
Sbjct: 1 KPVLTVYTYDSFAADWGPGPVVKKAFEADCNCELKLVALEDGVSLLNRLRLEGKNSKADV 60
Query: 89 VLGFDNNLIDLARKTGLFAKSNIDASQLKLPIKWDDDIFVPYDYGYLAFIYDKRQITQPP 148
VLG DNNL+D A KTGLFAKS + A + +P W++D FVP+DYGY AF+YDK ++ PP
Sbjct: 61 VLGLDNNLLDAASKTGLFAKSGVAADAVNVPGGWNNDTFVPFDYGYFAFVYDKNKLKNPP 120
Query: 149 KNFDELINSTKPWKIIYQDPRTSTLGLGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWT 208
++ EL+ S + W++IYQDPRTST GLGLLLW+QK+YGD++ Q W+K+A KT TVTKGW+
Sbjct: 121 QSLKELVESDQNWRVIYQDPRTSTPGLGLLLWMQKVYGDDAPQAWQKLAKKTVTVTKGWS 180
Query: 209 ESYGFFLKGESDFVLSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQL 268
E+YG FLKGESD VLSY+TSP +++L +D+Y AA FSEGHYLQ+EVAA+ SKQP+L
Sbjct: 181 EAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPEL 240
Query: 269 AQEFMQFMISPSFQRILPTTNWMYPVVDISMPDVYQAIRIPQKSLRFNAEETTRYRNQWI 328
AQ+F+QF++SP+FQ +PT NWMYPV ++++P ++ + P +L F E R WI
Sbjct: 241 AQKFLQFLVSPAFQNAIPTGNWMYPVANVTLPAGFEKLTKPATTLEFTPAEVAAQRQAWI 300
Query: 329 SSWQNAVSR 337
S WQ AVSR
Sbjct: 301 SEWQRAVSR 309
>gnl|CDD|130321 TIGR01254, sfuA, ABC transporter periplasmic binding protein, thiB
subfamily. The model describes thiamine ABC
transporter, periplasmic protein in bacteria and archae.
The protein belongs to the larger ABC transport system.
It consists of at least three components: the thiamine
binding periplasmic protein; an inner membrane permease;
an ATP-binding subunit. It has been experimentally
demonstrated that the mutants in the various steps in
the de novo synthesis of the thiamine and the
biologically active form, namely thiamine pyrophosphate
can be exogenously supplemented with thiamine, thiamine
monophosphate (TMP) or thiamine pyrophosphate (TPP).
Length = 304
Score = 377 bits (970), Expect = e-105
Identities = 152/304 (50%), Positives = 215/304 (70%), Gaps = 1/304 (0%)
Query: 29 KPVLTVYTYNSFVADEGAGPKIKQAFERKCNCELKLIGLSDGVALLNKLRMEGENSAADI 88
+PV+TVYTY+SF AD G GP +++AFE CNC++K + L D LLN+LR+EG+N AD+
Sbjct: 1 QPVVTVYTYDSFAADWGLGPVVEKAFEADCNCKVKFVALEDAGELLNRLRLEGKNPKADV 60
Query: 89 VLGFDNNLIDLARKTGLFAKSNIDASQLKLPIKWDDDIFVPYDYGYLAFIYDKRQITQPP 148
VLG DNNL++ A KTGL A S + ++ +P W++ F+P+DYGY+AF+YDK ++ PP
Sbjct: 61 VLGLDNNLLEAASKTGLLAPSGVALDKVNVPGGWNNATFLPFDYGYVAFVYDKNKLQNPP 120
Query: 149 KNFDELINSTKPWKIIYQDPRTSTLGLGLLLWIQKIYGDNSA-QVWKKIATKTATVTKGW 207
++ EL+ + +IYQDPRTS+ GLGLLLW+Q +YG++ A Q WK++ KT TVTKGW
Sbjct: 121 QSLKELVEPEQDLLVIYQDPRTSSPGLGLLLWMQSVYGEDDAPQAWKQLRKKTVTVTKGW 180
Query: 208 TESYGFFLKGESDFVLSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQ 267
+E+YG FL GE D VLSY+TSP +++L +D+Y A FSEGHYLQ+E AA+L +KQP+
Sbjct: 181 SEAYGTFLGGEYDLVLSYATSPAYHVLFEKKDNYAALNFSEGHYLQVEGAARLKGAKQPE 240
Query: 268 LAQEFMQFMISPSFQRILPTTNWMYPVVDISMPDVYQAIRIPQKSLRFNAEETTRYRNQW 327
LA +F+QF++SP+ Q +PT NWMYPVV+ ++ + + + E T R W
Sbjct: 241 LADKFVQFLLSPAVQNAIPTGNWMYPVVNGTLLPGFFKLTQQPTTTAPTPAEVTAQRQAW 300
Query: 328 ISSW 331
IS W
Sbjct: 301 ISEW 304
>gnl|CDD|132271 TIGR03227, PhnS, 2-aminoethylphosphonate ABC transporter,
periplasmic 2-aminoethylphosphonate binding protein.
This ABC transporter periplasmic substrate binding
protein component is found in a region of the salmonella
typhimurium LT2 genome responsible for the catabolism of
2-aminoethylphosphonate via the phnWX pathway
(GenProp0238). The protein contains a match to pfam01547
for the "Bacterial extracellular solute-binding protein"
domain.
Length = 367
Score = 45.9 bits (108), Expect = 2e-05
Identities = 34/165 (20%), Positives = 74/165 (44%), Gaps = 4/165 (2%)
Query: 28 AKPVLTVYTYNSFVADEGAGPKIK-QAFERKCNCELKLIGLSDGVALLNKLRMEGENSAA 86
A V+ VY+ + + + + + AFE+ ++ ++ G ++ + E N A
Sbjct: 34 AAAVVLVYSADGLEDGDNSLYQDQFDAFEKAEGIKVNIVEAGGGE-VVERAAKEKGNPKA 92
Query: 87 DIVLGFDNNLIDLARKTGLFAKSNIDA-SQLKLPIKWDDDIFVPYDYGYLAFIYDKRQIT 145
D+++ I A GL A N DA + K D ++ P+ Y +F + + +
Sbjct: 93 DVIVTAPP-FIQQAAAEGLLANFNSDAAKAIPAIAKAADGLWAPFVKNYFSFAINPKLLK 151
Query: 146 QPPKNFDELINSTKPWKIIYQDPRTSTLGLGLLLWIQKIYGDNSA 190
P +F +L+++ K+ Y +P + G+ +++ ++G A
Sbjct: 152 SAPASFADLLDADFKGKLAYSNPAQAADGMAVIILAFALFGSEDA 196
>gnl|CDD|185006 PRK15046, PRK15046, 2-aminoethylphosphonate ABC transporter
substrate-binding protein; Provisional.
Length = 349
Score = 43.1 bits (102), Expect = 1e-04
Identities = 32/139 (23%), Positives = 61/139 (43%), Gaps = 3/139 (2%)
Query: 53 AFERKCNCELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGLFAK-SNI 111
AF + ++ + G ++N+ E N AD+++ I A GL S++
Sbjct: 55 AFTKATGIKVNYVEAGSGE-VVNRAAKEKSNPQADVLVTLPP-FIQQAAAEGLLQPYSSV 112
Query: 112 DASQLKLPIKWDDDIFVPYDYGYLAFIYDKRQITQPPKNFDELINSTKPWKIIYQDPRTS 171
+A + K D + P+ YL+FIY+ + + P + +L++ K+ Y P +
Sbjct: 113 NAKAVPAIAKDADGTYAPFVNNYLSFIYNPKVLKTAPATWADLLDPKFKGKLQYSTPGQA 172
Query: 172 TLGLGLLLWIQKIYGDNSA 190
G +LL + G + A
Sbjct: 173 GDGTAVLLLTFHLMGKDKA 191
>gnl|CDD|163195 TIGR03261, phnS2, putative 2-aminoethylphosphonate ABC transporter,
periplasmic 2-aminoethylphosphonate-binding protein.
This ABC transporter extracellular solute-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely.
Length = 334
Score = 35.6 bits (82), Expect = 0.020
Identities = 74/314 (23%), Positives = 123/314 (39%), Gaps = 40/314 (12%)
Query: 6 RIVVGIMMITGVISYCTLDGLPAKPVLTVYTYNSFVADEGAGPKIKQAFERK-CNCELKL 64
+V G +M + S C A LTVYT ++ K K AFE+ + ++
Sbjct: 1 SVVAGFIMTSLFFSACNSK---ANTELTVYT----AIEDELIAKYKDAFEKVNPDIKINW 53
Query: 65 IGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLARKTGL---FAKSNIDASQLKLPIK 121
+ S G+ + KL E N AD+V G + + L K G+ + +DA L K
Sbjct: 54 VRDSTGI-ITAKLLAEKNNPQADVVWGLAASSLALLDKEGMLKPYKPKGLDA----LNPK 108
Query: 122 WDDDIFVPYDYGYLAF--------IYDKRQITQPPKNFDELINSTKP---WKIIYQDPRT 170
+ D P+ G A+ + K++ P ++++L TKP I+ +P +
Sbjct: 109 FRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDL---TKPEYKGHIVMPNPAS 165
Query: 171 STLG-LGLLLWIQKIYGDNSAQVWKKIATKTATVTKGWTESYGFFLKGESDFVLSYSTSP 229
S G L + W+Q + D K+ A T ++ GE +S +
Sbjct: 166 SGTGFLDVSAWLQMMGEDKGWDYMDKLHKNIAVYTHSGSKPCKLAGMGEFPIGISMAYRA 225
Query: 230 GFYLLNYGQDDYVAALF-SEGHYLQIEVAAQLVRSKQPQLAQEFMQFMISPSFQRILPTT 288
L + + +F EG IE A + SK A++ + + IS +
Sbjct: 226 ---LKEKKKGAPIDVVFPKEGLGWDIEATAIIKGSKNNDAAKKLVDWSIS---DEAMELY 279
Query: 289 NWMYPVVDISMPDV 302
Y VV + P V
Sbjct: 280 AKNYAVV--ATPGV 291
>gnl|CDD|183238 PRK11622, PRK11622, hypothetical protein; Provisional.
Length = 401
Score = 34.2 bits (79), Expect = 0.046
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 128 VPYDYGYLAFIYDKRQITQPPKNFDELINSTK--PWKIIYQDP 168
P+ L FIYD + QPP++ EL+ K P + Y P
Sbjct: 152 APWGGAQLVFIYDSARTPQPPQSPAELLEWAKANPGRFTYPRP 194
>gnl|CDD|181889 PRK09474, malE, maltose ABC transporter periplasmic protein;
Reviewed.
Length = 396
Score = 31.5 bits (72), Expect = 0.34
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 14/65 (21%)
Query: 102 KTGLFAKSNIDAS-QLKL-PIKWDDDIFVPYD---YGY------LAFIYDKRQITQPPKN 150
++GL A+ + + KL P WD V Y+ GY L+ IY+K + PPK
Sbjct: 98 QSGLLAEVTPSKAFKDKLVPFTWDA---VRYNGKLIGYPIAVEALSLIYNKDLVPTPPKT 154
Query: 151 FDELI 155
++E+
Sbjct: 155 WEEIP 159
>gnl|CDD|177842 PLN02190, PLN02190, cellulose synthase-like protein.
Length = 756
Score = 31.0 bits (70), Expect = 0.42
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 15/82 (18%)
Query: 223 LSYSTSPGFYLLNYGQDDYVAALFSEGHYLQIEVAAQLVRSKQPQLAQEFM-------QF 275
L Y P + LL+ +ALF +G YL I V LV EFM +
Sbjct: 547 LIYCLLPAYCLLHN------SALFPKGVYLGIIVT--LVGMHCLYTLWEFMSLGFSVQSW 598
Query: 276 MISPSFQRILPTTNWMYPVVDI 297
+S SF RI T++W++ + DI
Sbjct: 599 YVSQSFWRIKATSSWLFSIQDI 620
>gnl|CDD|150295 pfam09581, Spore_III_AF, Stage III sporulation protein AF
(Spore_III_AF). This family represents the stage III
sporulation protein AF (Spore_III_AF) of the bacterial
endospore formation program, which exists in some but
not all members of the Firmicutes (formerly called
low-GC Gram-positives). The C-terminal region of these
proteins is poorly conserved.
Length = 185
Score = 29.2 bits (66), Expect = 1.6
Identities = 6/19 (31%), Positives = 16/19 (84%)
Query: 1 MKKFARIVVGIMMITGVIS 19
MKK+ ++V+G+++I +++
Sbjct: 19 MKKYVKLVLGLLLIVIILN 37
>gnl|CDD|178202 PLN02592, PLN02592, ent-copalyl diphosphate synthase.
Length = 800
Score = 29.1 bits (65), Expect = 1.9
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 118 LPIKWDDDIFVPYDYGYLAFIYDKRQI--TQPPKNFDELINST 158
L I + DI VPYD L IY +R + T+ PK+ + +T
Sbjct: 200 LEIAKNLDIEVPYDSPVLKEIYAQRNLKLTRIPKDIMHKVPTT 242
>gnl|CDD|185296 PRK15398, PRK15398, aldehyde dehydrogenase EutE; Provisional.
Length = 465
Score = 28.7 bits (65), Expect = 1.9
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 82 ENSAADIVLG--FDNNLIDLARK 102
E +A DIV G FDNNL +A K
Sbjct: 254 EKAARDIVKGASFDNNLPCIAEK 276
>gnl|CDD|177653 PLN00014, PLN00014, light-harvesting-like protein 3; Provisional.
Length = 250
Score = 28.7 bits (64), Expect = 2.4
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 311 KSLRFNAEETTRYRNQWISSWQNA 334
+L+ A+E T Y QW ++W++
Sbjct: 218 DTLKKLADEATFYDKQWQATWKDQ 241
>gnl|CDD|128425 smart00115, CASc, Caspase, interleukin-1 beta converting enzyme
(ICE) homologues. Cysteine aspartases that mediate
programmed cell death (apoptosis). Caspases are
synthesised as zymogens and activated by proteolysis of
the peptide backbone adjacent to an aspartate. The
resulting two subunits associate to form an
(alpha)2(beta)2-tetramer which is the active enzyme.
Activation of caspases can be mediated by other caspase
homologues.
Length = 241
Score = 28.4 bits (64), Expect = 2.5
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 218 ESDFVLSYSTSPGFYL 233
E+DF+ +YST+PG+
Sbjct: 159 EADFLAAYSTTPGYVS 174
>gnl|CDD|161895 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however.
Length = 798
Score = 28.4 bits (64), Expect = 2.9
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 61 ELKLIGLSDGVALLNKLRMEGENSAADIVLGFDNNLIDLA 100
EL L SDG+ +L++ G + A LG D+++I+++
Sbjct: 125 ELGLDEKSDGIIVLDEDAPLGTDIAE--YLGLDDDIIEVS 162
>gnl|CDD|183199 PRK11561, PRK11561, isovaleryl CoA dehydrogenase; Provisional.
Length = 538
Score = 26.6 bits (59), Expect = 8.3
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 257 AAQLVRSKQPQLAQEFMQFMISPSFQRILP 286
AQ++R P LAQ + Q M+ L
Sbjct: 495 GAQMLRHASPPLAQAWCQMMLDTRGGVRLS 524
>gnl|CDD|162054 TIGR00815, sulP, high affinity sulphate transporter 1. (2) SO42-
(out) + nHCO3- (in) SO42- (in) + nHCO3- (out).
Length = 563
Score = 26.5 bits (59), Expect = 9.3
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 5 ARIVVGIMMITGVISYCTLDGLPAKPVLTVYTYNSFVA 42
A + VGI++I ++Y L GL P+ +YT SFV
Sbjct: 20 AGLTVGILLIPQAMAYAILAGLS--PIYGLYT--SFVP 53
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 0.137 0.414
Gapped
Lambda K H
0.267 0.0634 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,644,611
Number of extensions: 360104
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 650
Number of HSP's successfully gapped: 24
Length of query: 338
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 244
Effective length of database: 3,963,321
Effective search space: 967050324
Effective search space used: 967050324
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 (21.8 bits)
S2: 57 (25.9 bits)