Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 358 bits (918), Expect = e-103 Identities = 193/493 (39%), Positives = 304/493 (61%), Gaps = 9/493 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 L EM GI K+FPGVKALD+V+ + P +H L+GENGAGKS+L+K L G+Y D+G Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM--FVDQDKMYRET 130 G + S + + GI+++ QE +LV + N++LGR P + VD +M+ E Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEA 129 Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190 + I D L +++ R V L V+Q QM+EIAKA S NA+I+++DEPT++L+++E LF Sbjct: 130 RRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFA 189 Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250 +I +LK G ++YISH+M E+F L D +T+LRDG+ + T D+++A MVGR + Sbjct: 190 VIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRKV 249 Query: 251 NQRFP-DKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 + + ++ +PGEV L+VRN+++ I D++ + GEI+G+AGLVG+ R+++ + Sbjct: 250 DMSYSRERSAQPGEVALDVRNVSA--DSGIADINLQVRAGEIVGLAGLVGSGRSEVARAV 307 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 FG G I + GK++ + A G AL+ E R+S G+ + N L++ +R Sbjct: 308 FGADPIRQGEIYIFGKRLTG-GPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLRR 366 Query: 370 -YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEIL 428 + + D + ++ + I +R+ TP LSGGNQQK++IG+WL+ + ++ Sbjct: 367 AFPARWYRADKAEALAERE--IARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLF 424 Query: 429 MLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIV 488 + DEPTRGIDVGAK EI+ LI L K+G G+++ISSE+PE++ + DR VM G ++G V Sbjct: 425 IFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEV 484 Query: 489 DTKTTTQNEILRL 501 T+ IL+L Sbjct: 485 AHAEMTEERILQL 497 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: 600 Number of extensions: 38 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: 502 Length adjustment: 34 Effective length of query: 472 Effective length of database: 468 Effective search space: 220896 Effective search space used: 220896 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