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 BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 433 bits (1113), Expect = e-126 Identities = 231/493 (46%), Positives = 329/493 (66%), Gaps = 3/493 (0%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61 + IL++K + KRFPGV AL G+ ++ GEVHA+ GENGAGKSTLMKII+G Y+ DEG + Sbjct: 21 REILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVV 80 Query: 62 IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREA 121 Y G V+++ S+A AGI + QEL+++ +LSVAENI++ E KRG F+DY+ + A Sbjct: 81 RYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNA 140 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 ++ + + G+ + P +G S+A QQMVEIA+A+ A+VLI+DEPTSSLT+ ET +LF Sbjct: 141 QRCL-QRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLF 199 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 +++ L+ GVAI++ISHRL+E+ EI D+V+VLRDG +I T + T +IV MVGR Sbjct: 200 RIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRP 259 Query: 242 LEKFYIKEAHEPG-EVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIF 299 L+ Y P +++L V++L F +SF LR+GEILGFAGL+GAGRTE IF Sbjct: 260 LDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIF 319 Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359 G G I + + V I P +AI GI + EDRKK GL L M + N++L ++ I Sbjct: 320 GAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAI 379 Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419 F+ F E +A+ ++ IR + LSGGNQQK+V++KWL +IL D Sbjct: 380 SSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 439 Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479 EPTRGIDVGAK IY +M +LA +GVGV++ISSELPE+L M+DRIAV G++ +++ + Sbjct: 440 EPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETR 499 Query: 480 EASQEKVMKLAAG 492 + SQE+++ A+G Sbjct: 500 QTSQEEILHHASG 512 Score = 77.4 bits (189), Expect = 1e-18 Identities = 56/225 (24%), Positives = 107/225 (47%), Gaps = 9/225 (4%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 +S E GE+ G GAG++ + I G +PD G I V P EAI GI Sbjct: 291 LSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIA 350 Query: 83 TVFQELS---VMDNLSVAENIFMGDEE---KRGIFIDYKKMYREAEKFMKEEFGIEIDPE 136 + ++ + ++ V+ NI + + RG F+ + + AE++++E GI Sbjct: 351 YLSEDRKKDGLALSMPVSANITLANVRAISSRG-FLRFSEETAIAERYVRE-LGIRTPTV 408 Query: 137 EKLGK-YSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAII 195 +++ + S QQ + I++ +Y+ +++L DEPT + ++ ++ L GV ++ Sbjct: 409 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVV 468 Query: 196 FISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 IS L E+ + D+++V +G ++E+I+ GR Sbjct: 469 LISSELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASGR 513 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: 617 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: 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 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