Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 372 bits (956), Expect = e-107 Identities = 207/496 (41%), Positives = 316/496 (63%), Gaps = 6/496 (1%) Query: 1 MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60 M +E +++ K F V L GV PG V+ ++GENGAGKSTLMKI+AG P GE Sbjct: 1 MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60 Query: 61 IIYEGRGVRWNHPSEAINA-GIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYR 119 ++ +G S A A GIV + QE ++ D+L++A+NIF+G E KRG+F+D K M R Sbjct: 61 VVVDGAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAM-R 119 Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179 E + + G+ +DP+ ++ K +A +Q+VEIARA+ + A++LI+DEPT++LT ETE+ Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179 Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239 LF ++ LK GV II+ISH+L+E+ D+V V+RDG + ++ ++T+ ++ +MVG Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVG 239 Query: 240 RKLEKFYIKE--AHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELME 296 R+L + + A + G + V+ L+ + E V F +RRGEILGFAGLVGAGRTEL E Sbjct: 240 RELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFE 299 Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356 + G RP+ G + I G+ V++ P DA G+ + EDRK GL + + N++L +L Sbjct: 300 GLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMAL 359 Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416 +R K P++ E+ A++ F IR + + LSGGNQQK+ LAK L P ++ Sbjct: 360 ERYAK-PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVV 418 Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476 +LDEPTRG+DVGAK EIY ++ +LA++G+ VI+ISSEL E++ + R+AVM G+L + Sbjct: 419 VLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTL 478 Query: 477 DAKEASQEKVMKLAAG 492 ++E+++ A G Sbjct: 479 QEPHLTEEELIAHATG 494 Score = 89.7 bits (221), Expect = 2e-22 Identities = 71/245 (28%), Positives = 118/245 (48%), Gaps = 12/245 (4%) Query: 256 VVLEVKNLSGER-----FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310 V +E +N++ E V F+L+ G + G G GAG++ LM+ + G+ GE+ Sbjct: 3 VAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVV 62 Query: 311 IEGK-RVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKR 369 ++G R A QGI L+ ++ L ++I N+ L IK+G F+ K Sbjct: 63 VDGAVRAPGGGSRAAEAQGIVLIHQE---FNLADDLTIAQNIFLGH--EIKRGLFLDDKA 117 Query: 370 EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGA 429 +E A+ + P PD +V L +Q V +A+ LA ++LI+DEPT + G Sbjct: 118 MREKTREALAKVGL-PLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGE 176 Query: 430 KAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKL 489 ++ +M+ L GV +I IS +L EV + +D + VM G L ++ ++ L Sbjct: 177 TERLFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANL 236 Query: 490 AAGLE 494 G E Sbjct: 237 MVGRE 241 Score = 75.5 bits (184), Expect = 4e-18 Identities = 57/226 (25%), Positives = 109/226 (48%), Gaps = 6/226 (2%) Query: 21 KGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAG 80 +GV E GE+ G GAG++ L + + G+ G + G+ V+ P +A G Sbjct: 272 EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHG 331 Query: 81 IVTVFQELS---VMDNLSVAENI-FMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDP- 135 + + ++ + + + N+ M E ++D + A + +EFGI Sbjct: 332 LTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKPWLD-PAAEQAALREAVQEFGIRTGSL 390 Query: 136 EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195 E + S QQ + +A+ ++ V++LDEPT + +++ +V+ L E+G+A+I Sbjct: 391 EVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVI 450 Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 IS L E+ +C +V+V+R G T +LT+E+++ G + Sbjct: 451 VISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATGTR 496 Lambda K H 0.318 0.138 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 672 Number of extensions: 38 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 494 Length of database: 496 Length adjustment: 34 Effective length of query: 460 Effective length of database: 462 Effective search space: 212520 Effective search space used: 212520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory