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_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 363 bits (931), Expect = e-104 Identities = 195/499 (39%), Positives = 314/499 (62%), Gaps = 12/499 (2%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L++ IHK+F G+ L+ V + YPGE+HA++G+NGAGKSTL+K++ GV + G++ Sbjct: 17 PVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMR 76 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF----IDYKKMY 118 G+ V + P A GI TV+QE+++ NLSVAENIF G + GI ID+ ++ Sbjct: 77 LGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLH 136 Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178 + A + G++ID L Y +A+QQ+V IARA+ +++VLILDEPTSSL E + Sbjct: 137 QRARDLVAR-IGLQIDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195 Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238 KLFEV++ L+ +G++I+F++H L +++ + D+++VLR+G ++G ++L + ++ M+ Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255 Query: 239 GRKLEKFYIKEAHEPGEVVLEVKNLSGE------RFENVSFSLRRGEILGFAGLVGAGRT 292 GR L + A P L E + + + +R GE++G AGL+G+GRT Sbjct: 256 GRDLAAASEQPAPAPAVDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSGRT 315 Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352 EL +FG G + I+G+ V+ +P+DAI G+ L PE+RK G++ +S+ N++ Sbjct: 316 ELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIA 375 Query: 353 LPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALK 412 L R+ G F+S + ELA+ +K I+ D+ + LSGGNQQK +LA+W+A++ Sbjct: 376 LALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMAIE 435 Query: 413 PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKL 472 P++LILDEPTRGIDV AK EI + +LA+ G+ V+ ISSE+ EV++++ RI V+ + Sbjct: 436 PRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRK 495 Query: 473 AGIIDAKEASQEKVMKLAA 491 G + A +S++ V L A Sbjct: 496 VGELPA-GSSEDAVYDLIA 513 Score = 77.0 bits (188), Expect = 1e-18 Identities = 61/229 (26%), Positives = 111/229 (48%), Gaps = 14/229 (6%) Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329 +V +L GEI G GAG++ L++ + G GG++ + G+ V + PL A GI Sbjct: 36 DVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMRLGGQAVWPDSPLAAQRLGI 95 Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDR--IKKGPFISF----KREKELADWAIKTFDI 383 V ++ + L +S+ N+ R I +G I + +R ++L D+ Sbjct: 96 STVYQE---VNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLHQRARDLVARIGLQIDV 152 Query: 384 RPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKE 443 D V QQ V +A+ L+++ ++LILDEPT +D +++ ++ +L E Sbjct: 153 TRLLSDYPVAV-----QQLVAIARALSIESRVLILDEPTSSLDDDEVQKLFEVLRRLRSE 207 Query: 444 GVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492 G+ ++ ++ L +V +SDRI V+ G G AK+ + ++ G Sbjct: 208 GLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAMLG 256 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: 610 Number of extensions: 22 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 494 Length of database: 517 Length adjustment: 34 Effective length of query: 460 Effective length of database: 483 Effective search space: 222180 Effective search space used: 222180 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