Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate BPHYT_RS12995 BPHYT_RS12995 MFS transporter
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__BFirm:BPHYT_RS12995 Length = 489 Score = 214 bits (546), Expect = 5e-60 Identities = 117/311 (37%), Positives = 181/311 (58%), Gaps = 12/311 (3%) Query: 18 RRVIFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLGFAAGFAVRPFGA 77 +R + A +LG EW+DF + +A+ + + FF +PAA + T FAA F VRP G Sbjct: 32 KRAVGAMALGNAMEWFDFGVYSYIAVTLGKVFFPSASPAAQLIATFGTFAAAFLVRPVGG 91 Query: 78 IVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALGG 137 +VFG LGD IGR+ T+++M L TF +GL+P Y TIG+ AP++ + R++QG + GG Sbjct: 92 MVFGPLGDRIGRQRVLAMTMIMMALGTFAIGLIPSYTTIGIFAPMLLLVARLVQGFSTGG 151 Query: 138 EYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAAWGWRVP 197 EYGGAAT++AE + +RG ++++ +G + + + + L+ D +WGWRVP Sbjct: 152 EYGGAATFIAEFSTDKRRGFMGSFLEFGTLIGYVLGAGTVAVLTATLSNDALLSWGWRVP 211 Query: 198 FLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTS--KAPLSEAFG-----QWKNLKIVLL 250 FL++ L V ++IRM+L E+P F++ +AE + + KA ++FG QWK LL Sbjct: 212 FLIAGPLGLVGLYIRMKLEETPAFKK-QAEQREAEDKAVPKQSFGQLLAQQWK----PLL 266 Query: 251 ALFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFFLFFGSLSDKI 310 GL V Y Y +L+ TL + T LV + +++ P L G LSD I Sbjct: 267 LCVGLVLIFNVTDYMALSYLPSYLSATLHFNETHGLFLVLLVMVLMMPMTLAAGRLSDTI 326 Query: 311 GRKPIIMAGCL 321 GRKP+++ GC+ Sbjct: 327 GRKPVMLFGCV 337 Score = 41.6 bits (96), Expect = 7e-08 Identities = 28/110 (25%), Positives = 57/110 (51%), Gaps = 6/110 (5%) Query: 439 GYPAKADPALINWPMSILI-----LTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPY 493 G A + PAL+ M ++ L IL + ++ G + + L +FP +IRY ++++ + Sbjct: 338 GLFALSIPALLLIRMGTVLPVFGGLMILGVLLSCFTGVMPSALPALFPTKIRYGALAIGF 397 Query: 494 HIGNGWFGGFLPATAFAIIAARGNIYSGLWYPIVIASVAFVIGTLFVKET 543 +I FGG P ++ GN+ +Y ++ AS+ ++ + ++ET Sbjct: 398 NISVSLFGGTTPLVTAWLVDRTGNLMMPAYY-LMGASLIGIVSVVALRET 446 Score = 27.7 bits (60), Expect = 0.001 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 8/88 (9%) Query: 251 ALFGLTAGQAVVWYTGQFYTLFFLT--QTLKVDGTSANMLVAV------ALLIGTPFFLF 302 A+ + G A+ W+ Y+ +T + + A L+A A L+ + Sbjct: 34 AVGAMALGNAMEWFDFGVYSYIAVTLGKVFFPSASPAAQLIATFGTFAAAFLVRPVGGMV 93 Query: 303 FGSLSDKIGRKPIIMAGCLIAALTYFPL 330 FG L D+IGR+ ++ ++ AL F + Sbjct: 94 FGPLGDRIGRQRVLAMTMIMMALGTFAI 121 Lambda K H 0.325 0.139 0.420 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: 626 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 552 Length of database: 489 Length adjustment: 35 Effective length of query: 517 Effective length of database: 454 Effective search space: 234718 Effective search space used: 234718 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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