Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_012385743.1 BIND_RS14235 sugar ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_000019845.1:WP_012385743.1 Length = 511 Score = 470 bits (1210), Expect = e-137 Identities = 249/494 (50%), Positives = 341/494 (69%), Gaps = 3/494 (0%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70 +YLL I K FPGV ALD V LK+R S+HALMGENGAGKSTL+K + GIY+ D+G I Sbjct: 19 DYLLTAENIRKEFPGVLALDGVELKLRRSSVHALMGENGAGKSTLMKIIAGIYKPDAGRI 78 Query: 71 LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRE 129 +G EI F S +ALE+GISM+HQELNL+ +V +N+W+ R P FVD D+M R Sbjct: 79 RLKGNEISFQSPLDALESGISMIHQELNLMDYMTVAENIWIRREPLNRFGFVDHDEMRRM 138 Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189 T+A+F L ID+DP A V LSV+ Q++EIAKA SY + ++IMDEPTS+LTE+EV+HLF Sbjct: 139 TQALFRRLRIDLDPDAEVRDLSVANRQIVEIAKAVSYGSDVLIMDEPTSALTEREVDHLF 198 Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 IIR L+ +G GIVYI+HKM E+F++ DE ++ RDG++I+T +T D II MMVGR Sbjct: 199 EIIRDLRAQGIGIVYITHKMNELFEIADEFSIFRDGRYISTHAACDVTCDDIIRMMVGRE 258 Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 L Q FP +E G+V L V+N+ + V+FDL GEILGIAGL+G+ R+ + TL Sbjct: 259 LTQMFPKEEVPIGDVALSVKNVGL--DGVFQGVNFDLRAGEILGIAGLIGSGRSSLAATL 316 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 FG+ ++G+I + G + + A+ H A +TE+R+ +G L I N ++ +++ Sbjct: 317 FGVTPATSGSIAIAGNDVVIDSPATAMRHQMAFLTEDRKVSGCLLSLSILENLQLAVLQD 376 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 G + + S + +RVKTP + IG+LSGGNQQKV+IGRWLL +P IL+ Sbjct: 377 KYVTNGFVHEKELFSACDEMARKLRVKTPNLQEIIGNLSGGNQQKVLIGRWLLNKPRILI 436 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 LDEPTRGIDVGAK EI++L+ ELA++G II+ISSEMPE+LG++DRI+VM G ++GI+D Sbjct: 437 LDEPTRGIDVGAKAEIHRLVTELAREGVAIILISSEMPEVLGMSDRIMVMHEGRMTGILD 496 Query: 490 TKTTTQNEILRLAS 503 TQ +I+ LAS Sbjct: 497 RSEATQVKIMELAS 510 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: 638 Number of extensions: 20 Number of successful extensions: 6 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: 511 Length adjustment: 34 Effective length of query: 472 Effective length of database: 477 Effective search space: 225144 Effective search space used: 225144 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