Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 389 bits (1000), Expect = e-112 Identities = 199/469 (42%), Positives = 308/469 (65%), Gaps = 4/469 (0%) Query: 10 LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69 L EG+SKFFPGVKALDNV +R G + AL+GENGAGKSTL+K L G+Y D+G I ++ Sbjct: 6 LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65 Query: 70 GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129 G+ + ++T A + GI ++QE+NL+P+M+VA+N+++GREP ++G + +++ ++ +L Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125 Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189 + L + S+A QQ+V I +A+ +A ++I+DEPT++L EV LF ++R Sbjct: 126 LDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIR 185 Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTH 249 LR +G ++I+++H +D+++ ++D I+V R+G++VG ++T E + L+ M+GREL T Sbjct: 186 DLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGREL-TQ 244 Query: 250 ALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGI 309 + + + V +N +KG + VR GEI+G+AGL+G+GR+E E +FG+ Sbjct: 245 LFPKFNNAI--GEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGM 302 Query: 310 KPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENI-ILALQAQRG 368 + ADSG LI G P N+ SP A G+ EDRK G+ SV EN+ I+ + G Sbjct: 303 EKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIG 362 Query: 369 WLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDE 428 + + E IR+L I+TP+ +Q I LSGGNQQKVL++RWLL +P+ LILDE Sbjct: 363 KTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDE 422 Query: 429 PTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477 PTRGIDVGA AEI LI L G+A++++SSEL E++G +DRV++M + Sbjct: 423 PTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHE 471 Score = 99.0 bits (245), Expect = 3e-25 Identities = 67/227 (29%), Positives = 121/227 (53%), Gaps = 13/227 (5%) Query: 7 QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66 +E+L LS+ A +++FS+RRGEI+ + G GAG+S ++++L G+ AD G + Sbjct: 255 EEVLTVRNLSR----KGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEV 310 Query: 67 WLEGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFGLLRRKEME 123 ++G ++ + + A + G+ + ++ L +SV +N+ I + P+ G + Sbjct: 311 LIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHL 370 Query: 124 KRATELMASYGFSLDVREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDT 178 K A + M L+++ P +N S QQ V I R + K+LILDEPT +D Sbjct: 371 KMAEDCMEQIR-RLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDV 429 Query: 179 QEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVG 225 ++ L+ +L +RGV++I V+ L ++ +SDR+ V+ G G Sbjct: 430 GAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITG 476 Lambda K H 0.321 0.138 0.391 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: 600 Number of extensions: 30 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: 500 Length of database: 494 Length adjustment: 34 Effective length of query: 466 Effective length of database: 460 Effective search space: 214360 Effective search space used: 214360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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