Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS16930 BPHYT_RS16930 arabinose ABC transporter ATP-binding protein
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__BFirm:BPHYT_RS16930 Length = 512 Score = 389 bits (999), Expect = e-112 Identities = 210/494 (42%), Positives = 309/494 (62%), Gaps = 10/494 (2%) Query: 14 LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73 L I K FPGV+ALD V+ V +H LMGENGAGKSTLLK L G YQ DSG ++ Sbjct: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 Query: 74 GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133 G E+ F SA ++ GI+++HQEL V +V +N+ LG+ P +V++ + R + Sbjct: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193 + + + +DP A++ LS++Q QM+EI KA NA+++ +DEPTSSL+ +E LF ++R Sbjct: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 Query: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEP-LAGLTMDKIIAMMVGRSLNQ 252 L+ ++YISH+M+EI++LCD T+ RDG+ IA+ P L G+T D I++ MVGR ++ Sbjct: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 Query: 253 RFPDKENKPGEVILEVRNLT--SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310 + GEV + + +L QP+ SF++ +GEI+G GLVGA R++++ ++ Sbjct: 245 IYNYSARPLGEVRFAAKGIEGHALAQPA----SFEVRRGEIVGFFGLVGAGRSELMHLVY 300 Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370 G K G + L GK I +A EAI HG L E+R+ GI A + N IS R+Y Sbjct: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360 Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE--IL 428 LD + I +++KTP R +I LSGGNQQK I+ RW L +P+ ++ Sbjct: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVV 419 Query: 429 MLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIV 488 +LDEPTRGIDVGAK EIY +I +LA++G I++ISSE+PE+LG++DRI+VM G +SG + Sbjct: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479 Query: 489 DTKTTTQNEILRLA 502 K T+ +L LA Sbjct: 480 TRKDATEQSVLSLA 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: 584 Number of extensions: 23 Number of successful extensions: 8 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: 512 Length adjustment: 34 Effective length of query: 472 Effective length of database: 478 Effective search space: 225616 Effective search space used: 225616 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