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 AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 361 bits (927), Expect = e-104 Identities = 200/498 (40%), Positives = 304/498 (61%), Gaps = 11/498 (2%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L ++ + K F GV AL GV GE+HA++GENGAGKSTL+K + GVYQ D G + Sbjct: 11 PLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVT 70 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 EGR + EA I TV+QE++++ NLSVAEN+F+G + R +D M R A Sbjct: 71 LEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRAR 130 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + +G+ +D LG++S+A QQ+V IARAV AKVLILDEPT+SL +E LF+ Sbjct: 131 AVLIP-YGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFK 189 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 V+++L+ +G+ I+F++H L++++ +CD+++VLR+G +G L + +V MM+GR+L Sbjct: 190 VMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGREL 249 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGERF---------ENVSFSLRRGEILGFAGLVGAGRTE 293 E + A P + E RF E +R GE++G AGL+G+GRTE Sbjct: 250 EAVAHRIA-PPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTE 308 Query: 294 LMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL 353 +FG GE ++G+ V + P DAI G G PEDRKK G++ +S+ N+ L Sbjct: 309 TARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIIL 368 Query: 354 PSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413 R I R++E+AD I+ DIR + ++ + LSGGNQQK +LA+WLA +P Sbjct: 369 ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEP 428 Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473 ++LILDEPTRGIDVGA AEI R++ +L +G+ ++++SSEL E++ S R+ V+ + Sbjct: 429 RLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHV 488 Query: 474 GIIDAKEASQEKVMKLAA 491 + E + ++++ A Sbjct: 489 AELRGGEVAVDRIVAAIA 506 Score = 79.3 bits (194), Expect = 3e-19 Identities = 60/235 (25%), Positives = 111/235 (47%), Gaps = 12/235 (5%) Query: 263 LSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPL 322 L + + V F++R GEI G GAG++ L++T+ G + G + +EG+ + Sbjct: 23 LGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLEGRAIAPRGVE 82 Query: 323 DAIEQGIGLVPEDRKKLGLILIMSIMHNVSL---PSLDRIKKGPFISFKREKELADWAIK 379 +A IG V ++ + L+ +S+ N+ L P + + + L + + Sbjct: 83 EAQRLHIGTVYQE---VNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARAVLIPYGL- 138 Query: 380 TFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQ 439 T D+ V QQ V +A+ + + K+LILDEPT +D A ++++M Sbjct: 139 TLDVTAPLGRFSV-----ATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMRT 193 Query: 440 LAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 L G+G++ ++ L +V + DRI V+ G+L G E + ++ + G E Sbjct: 194 LRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRE 248 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: 622 Number of extensions: 32 Number of successful extensions: 8 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: 516 Length adjustment: 34 Effective length of query: 460 Effective length of database: 482 Effective search space: 221720 Effective search space used: 221720 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 Apr 09 2024. 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