Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_040662390.1 ON16_RS11055 sugar ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_000307265.1:WP_040662390.1 Length = 499 Score = 439 bits (1129), Expect = e-127 Identities = 225/493 (45%), Positives = 328/493 (66%), Gaps = 2/493 (0%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70 EY++EM INKSF GV L NV ++ + AL+GENGAGKSTL+K L G+Y +DSGT+ Sbjct: 3 EYIVEMENINKSFSGVPVLKNVRFTLKAGEVMALLGENGAGKSTLMKILSGVYVRDSGTM 62 Query: 71 LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130 G+E K+A E G++++HQELN+ +V +N++LGR KG+ ++ +M + T Sbjct: 63 KIFGEEQGDLDTKKAQELGVAIIHQELNMCRHLTVAENIFLGREVRKGVTLNNREMVKRT 122 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + + D L ID+ P VG L VS+ QM+EIAKA S +AKI+IMDEPTS+L+ KE++ LF Sbjct: 123 QEVLDSLKIDLSPNTVVGDLPVSKQQMVEIAKALSVHAKILIMDEPTSALSSKEIDELFR 182 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250 ++ +L+ GCGIVYISH+MEE+ + + VTV+RDG++I A TMD++IA MVGR + Sbjct: 183 LVDQLRSEGCGIVYISHRMEELSHVANRVTVMRDGEFIMEGNFADYTMDQLIAKMVGRDI 242 Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310 ++FP + + GE ILEV+NL + R +RDVSFDL+ GEI+GIAGLVGA RT+ +F Sbjct: 243 KEKFPRVQCQRGEKILEVKNLNAGRM--VRDVSFDLYAGEIVGIAGLVGAGRTETTRAIF 300 Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370 GI K +G I L GK ++ +AI G L E+R+ G+ L + N I N+ Sbjct: 301 GIDPKDSGEIVLDGKSVSIKKPIDAIKAGIVLTPEDRKRDGLCTKLGVRENLSIPNLDWL 360 Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430 N +G ++ + + V++ +++K SLSGGNQQKV+IG+WL ++M Sbjct: 361 SNGIGKVNQKKEREIADKVVEELQIKLSSVEINAESLSGGNQQKVVIGKWLARNSRVIMF 420 Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490 DEPTRG+DVGAK EIY L+ L ++G G++ +SSE+PE+LGI+DRILVM +G ++G + Sbjct: 421 DEPTRGVDVGAKVEIYNLMNRLKQQGTGVLFVSSELPEILGISDRILVMCDGHLTGELPV 480 Query: 491 KTTTQNEILRLAS 503 T+++IL A+ Sbjct: 481 AEATEDKILSYAT 493 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: 619 Number of extensions: 21 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 472 Effective length of database: 465 Effective search space: 219480 Effective search space used: 219480 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 24 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