Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_040660822.1 ON16_RS07570 ATP-binding cassette domain-containing protein
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_000307265.1:WP_040660822.1 Length = 499 Score = 607 bits (1565), Expect = e-178 Identities = 299/497 (60%), Positives = 389/497 (78%), Gaps = 2/497 (0%) Query: 11 EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70 E LL+M+ I+K FPGVKALD+V+L V+P ++HALMGENGAGKSTL+KCLFGIY KD G I Sbjct: 4 EVLLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDEGKI 63 Query: 71 LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMYRE 129 +GKE+ F S+KEA+E+G++MVHQELN L+RSVMDN+WLGRYPT G+ V++ KMY + Sbjct: 64 FLEGKEVSFKSSKEAMESGVAMVHQELNQALKRSVMDNIWLGRYPTIGGVMVNEKKMYAD 123 Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189 TKAIFD+L ID+DP + T+ VSQ QM+EIAKA SYN+K+V+ DEPTSSLTE+EV HLF Sbjct: 124 TKAIFDDLGIDVDPHRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVEHLF 183 Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 II L++RG GI+YISHKM EI Q+ DEVT++RDG W+AT+ L II +MVGR Sbjct: 184 RIINMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMVGRE 243 Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 L +FP K N PGEV LEV +LT+ + + DVSF +GEILG+AGL + RT+ +E + Sbjct: 244 LGNQFPIKTNTPGEVYLEVEHLTA-QYSQLEDVSFSARRGEILGLAGLDASGRTETLENI 302 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 FGI + +GTI L G+++ N N+ E+I +GFAL+TEERR+TGI+ L I N++IS+++ Sbjct: 303 FGIATRKSGTIRLGGREVKNRNSRESIRNGFALLTEERRATGIFGILSIRENTVISSLKK 362 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 + +L++ M+ DTQW ID+MR KTP T+I SLSGGNQQKVI+GRWLLT PE+L+ Sbjct: 363 HLRAGFILNDKTMRQDTQWSIDAMRTKTPSQHTKIRSLSGGNQQKVILGRWLLTNPEVLL 422 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 LDEPTRGIDVGAKFEIYQLI +LA KGK ++++SSEMPELLG+ DRILVMS G ++G VD Sbjct: 423 LDEPTRGIDVGAKFEIYQLIIDLANKGKTVLMVSSEMPELLGVCDRILVMSGGRLAGEVD 482 Query: 490 TKTTTQNEILRLASLHL 506 K+TTQ EI+ LA+ ++ Sbjct: 483 AKSTTQEEIMTLAAKYV 499 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: 658 Number of extensions: 23 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