Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 416 bits (1069), Expect = e-120 Identities = 215/502 (42%), Positives = 339/502 (67%), Gaps = 9/502 (1%) Query: 9 SGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD-S 67 +G LEM I+++FPGVKALD VNL++R + AL GENGAGKSTL+K L GIY D Sbjct: 5 TGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPG 64 Query: 68 GTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYP-TKGMFVDQDKM 126 GTIL +G+E+ + A G+++++QEL +V +V +N++L R P T+ +D+ +M Sbjct: 65 GTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRM 124 Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 YRE + + +D+DIDP RV LSV Q QMIEIAKA +K +IMDEPT+SL+ E + Sbjct: 125 YREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETS 184 Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246 L I+++L+ER +VYISH++EEIF+L D VTVLRDG+ + T P+A +T + ++ +MV Sbjct: 185 VLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244 Query: 247 GRSLNQRFPDKENKPG-EVILEVRNLT----SLRQPSIRDVSFDLHKGEILGIAGLVGAK 301 R L++ + + ++ + +LEVR L+ +P IRD+SF LH+GE+LGIAGLVG+ Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304 Query: 302 RTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFN 361 RT+I+E +FG+R G++ + GK ++ N ++AI G VTE+R++ G+ + + N Sbjct: 305 RTEIMEMIFGMR-ACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVREN 363 Query: 362 SLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421 ++++ Y + + ++R + + + + +KTPG ++ +LSGGNQQK++I +W+ Sbjct: 364 FSLTHLERY-SPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWV 422 Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481 P++L++DEPTRGIDVGAK E++ LIA LA +G G+I+ISS++ E+L ++DRIL + Sbjct: 423 ARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVRE 482 Query: 482 GLVSGIVDTKTTTQNEILRLAS 503 G +SG + +Q +++ LA+ Sbjct: 483 GRISGELSRAQASQEKVMALAT 504 Lambda K H 0.318 0.136 0.384 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: 579 Number of extensions: 37 Number of successful extensions: 10 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: 506 Length of database: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 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