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 H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Burk376:H281DRAFT_03380 Length = 515 Score = 436 bits (1122), Expect = e-127 Identities = 234/493 (47%), Positives = 330/493 (66%), Gaps = 3/493 (0%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61 + IL++K + KRFPGV AL G+ ++ GEVHA+ GENGAGKSTLMKII+G Y D+G I Sbjct: 20 REILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVI 79 Query: 62 IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREA 121 YEG+ V++ S+A AGI + QEL+++ +LSVAENI++ E KRG F+DY+ + A Sbjct: 80 CYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANA 139 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 ++ + + G+ + P +G SIA QQMVEIA+A+ A+VLI+DEPTSSLT+ ET +LF Sbjct: 140 QRCL-QRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLF 198 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 +++ L+ GVAI++ISHRL+E+ EI D+V+VLRDG +I T + T +IV MVGR Sbjct: 199 RIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRA 258 Query: 242 LEKFYIKEAHEPGE-VVLEVKNLSG-ERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299 L+ Y P E V++ V++L + F +SF LR+GEILGFAGL+GAGRTE+ IF Sbjct: 259 LDDAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIF 318 Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359 G G I + V I P +AI GI + EDRKK GL L M + N++L ++ I Sbjct: 319 GAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAI 378 Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419 F+ F E +A+ ++ IR + LSGGNQQK+V++KWL +IL D Sbjct: 379 SSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 438 Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479 EPTRGIDVGAK IY++M +LA +GVGV++ISSELPE+L M+DRIAV G + +++ + Sbjct: 439 EPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETR 498 Query: 480 EASQEKVMKLAAG 492 + SQE+++ A+G Sbjct: 499 QTSQEEILHYASG 511 Score = 71.2 bits (173), Expect = 8e-17 Identities = 54/225 (24%), Positives = 107/225 (47%), Gaps = 9/225 (4%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 +S + GE+ G GAG++ + + I G + D G I V P EAI GI Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349 Query: 83 TVFQELS---VMDNLSVAENIFMGDEE---KRGIFIDYKKMYREAEKFMKEEFGIEIDPE 136 + ++ + ++ VA NI + + RG F+ + + AE++++E I Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSNVRAISSRG-FLRFSEETAIAERYVRE-LAIRTPTV 407 Query: 137 EKLGK-YSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195 +++ + S QQ + I++ +Y+ +++L DEPT + +++++ L GV ++ Sbjct: 408 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVV 467 Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 IS L E+ + D+++V +G ++E+I+ GR Sbjct: 468 LISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASGR 512 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: 627 Number of extensions: 28 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: 515 Length adjustment: 34 Effective length of query: 460 Effective length of database: 481 Effective search space: 221260 Effective search space used: 221260 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