Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__BFirm:BPHYT_RS16060 Length = 506 Score = 375 bits (963), Expect = e-108 Identities = 199/494 (40%), Positives = 301/494 (60%), Gaps = 5/494 (1%) Query: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 +L++ I KSFPGVKAL ++L++ IHAL+GENGAGKSTL+K L GIYQ D GTI Sbjct: 4 ILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTITI 63 Query: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRETK 131 +G+ F + +A+ G+ +V QE +L+ + ++NM+LGR G+ +++ KM R Sbjct: 64 EGEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGLGLLERGKMRRAAA 123 Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 AIF L + ID + LSV+Q Q +EI KA S A+I+I+DEPT++LT E HLF I Sbjct: 124 AIFQRLGVTIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAEHLFAI 183 Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 +R+LK++G +++ISH +EEIF++CD +TVLRDGQ++ +A + ++ MMVGR + Sbjct: 184 MRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMMVGRRIE 243 Query: 252 QRFPDKE--NKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309 FP K +++L+V L L+ + +SF L +GEILG AGLVG+ RT+ + Sbjct: 244 NSFPPKPPLRADAKIVLDVEKLQLLKDSPV--LSFTLREGEILGFAGLVGSGRTETALAV 301 Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369 G I ++G + +A+ G ++ E R++ G+ I N I+N+ Sbjct: 302 IGADPAYVKEIRINGTAAKLSDPADALRAGVGILPESRKTEGLITDFSIKQNISINNLGK 361 Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429 Y++ +D T ++ + VK P T++ +LSGGNQQKV+I RWL IL+ Sbjct: 362 YRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNHHTNILI 421 Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489 DEPTRGIDVGAK EIY L+ EL +G II+ISSE+PE++G+ DR+ V G + +++ Sbjct: 422 FDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGRIEAMLE 481 Query: 490 TKTTTQNEILRLAS 503 N ++ A+ Sbjct: 482 GDAIDSNAVMTYAT 495 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: 583 Number of extensions: 23 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: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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