Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 334 bits (856), Expect = 5e-96 Identities = 181/482 (37%), Positives = 291/482 (60%), Gaps = 10/482 (2%) Query: 7 QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66 Q L ++K FPGVKAL +V SL G++ AL+GENGAGKST++K LTG+Y D G I Sbjct: 18 QAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRI 77 Query: 67 WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPK-RFGLLRRKEMEKR 125 ++GQ + A G+ ++QE L +SVA+N+F+G P+ FGL+ K+ + Sbjct: 78 LVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTEN 137 Query: 126 ATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLF 185 A L+ S G LD L +A + +VAI RA+ + A+V+I+DEPTA+L +E+E L+ Sbjct: 138 ARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELY 197 Query: 186 DLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE 245 +L+ L+ +G +++F++H D++++++D TV R+G +G ++ + +LVKMM+GR+ Sbjct: 198 ELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRD 257 Query: 246 LDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305 + QRA V + Y +R GEI+G GL+G+GR+E + Sbjct: 258 VSQIFPQRAPNV---GDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQS 314 Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENII---LA 362 +FGI +G+ I G + SP A GI + PEDR G I + +N+ L Sbjct: 315 LFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLG 374 Query: 363 LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422 +++G+LR E+ +A + +L +R S + + LSGGNQQKV++++WL TRP+ Sbjct: 375 RISRKGFLR---LAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPR 431 Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVA 482 +ILDEPT+G+D+G+ A + + L A GLA++++SSE+ E++G +DRVI+MR+ + VA Sbjct: 432 VIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVA 491 Query: 483 EI 484 E+ Sbjct: 492 EL 493 Score = 83.6 bits (205), Expect = 2e-20 Identities = 57/215 (26%), Positives = 104/215 (48%), Gaps = 5/215 (2%) Query: 276 IAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVL 335 ++ L + PG++ L G G+G++ +++ GI D G L+ G+P +P A+ Sbjct: 36 LSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFSTPQAAADH 95 Query: 336 GIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPS 395 G+ ++ + SV ENI L A RG I K+ E A + +G Sbjct: 96 GVTAIHQETV---LFDELSVAENIFLG-HAPRGAFGLIDWKKTTENARALLTSIGAEL-D 150 Query: 396 TEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLAL 455 + ++ L N+ V ++R L + +I+DEPT + E+ L+E+L A G A+ Sbjct: 151 PDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLKAQGKAI 210 Query: 456 LVISSELEELVGYADRVIIMRDRKQVAEIPLAELS 490 L IS + +E+ AD + RD + + + +A+++ Sbjct: 211 LFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVT 245 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: 570 Number of extensions: 33 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 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