Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 360 bits (925), Expect = e-104 Identities = 198/491 (40%), Positives = 296/491 (60%), Gaps = 11/491 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +LR EG+SK + AL+NV F L GE+ AL+GENGAGKSTL+K L+G D G I++ Sbjct: 9 LLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGVIFI 68 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRF-GLLRRKEMEKRAT 127 +GQAI + A++ GI ++QE+N +P+M+VA+NLF+G+EP F G+L RK M + A Sbjct: 69 DGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHREAK 128 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 E + +D + PL S+ QQ+V I RA+ +AKVL+LDEPTA+L E L+ L Sbjct: 129 EKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQLYRL 188 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGR--- 244 + Q+R GV +++++H +++V+Q+++R+TV R+G+++G + ++V+MM+GR Sbjct: 189 IAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMVGRQIV 248 Query: 245 ELDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304 +L H + G LL + +A P EV GE+V ++GL+GSGRTE A Sbjct: 249 DLYQHEPRTPGDVLLEVRDLAG-------SATGPVSFEVSAGEVVSMSGLVGSGRTEVAR 301 Query: 305 VIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364 ++FG P G+ + G+ P A GIG EDRKT G+ SV NI ++ Sbjct: 302 LLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSL 361 Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424 + RK + +R+L +R + E P+ LSGGNQQK L+RWLL + L Sbjct: 362 DNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLL 421 Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEI 484 ILDEPTRG+D+GA EI LI+ L G A+LVISS+L E +G +DRV++MR + V ++ Sbjct: 422 ILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQL 481 Query: 485 PLAELSVPAIM 495 P + +M Sbjct: 482 PSCSATEEEVM 492 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: 584 Number of extensions: 26 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 500 Length of database: 510 Length adjustment: 34 Effective length of query: 466 Effective length of database: 476 Effective search space: 221816 Effective search space used: 221816 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