Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::P0AAG8 (506 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 397 bits (1019), Expect = e-115 Identities = 213/499 (42%), Positives = 315/499 (63%), Gaps = 8/499 (1%) Query: 12 YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GT 69 YLLEM I K+F VKA+DNV L++ I +L GENG+GKSTL+K L GIY S G Sbjct: 3 YLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62 Query: 70 ILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRE 129 I+F G+EI ++ GI+++HQEL LV + +V++N++LG T +D D M Sbjct: 63 IIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLR 122 Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189 + + ++ + I P RVG L + Q Q++EIAKA + +++I+DEPT+SLTE+E + L Sbjct: 123 CQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILL 182 Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249 IIR L++ G +YISHK+ E+ + D + V+RDGQ I T AG++ D II MMVGR Sbjct: 183 DIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRE 242 Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPS-----IRDVSFDLHKGEILGIAGLVGAKRTD 304 L +P++ + G+ IL + +LT+ + + DVSF L +GEILGIAGLVGA RT+ Sbjct: 243 LTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTE 302 Query: 305 IVETLFGI-REKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSL 363 ++ LFG+ + G I + GKQ++ N +AI G A+V E+R+ GI + +G N Sbjct: 303 TIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNIT 362 Query: 364 ISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLT 423 ++ + + + LD++ + I ++VKT IG LSGGNQQK I+ R LL Sbjct: 363 LAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLL 422 Query: 424 QPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGL 483 P IL+LDEPTRGID+GAK+EIY+LI +L ++G +I+ISSE+PE+LG++DR+LVM G Sbjct: 423 NPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGK 482 Query: 484 VSGIVDTKTTTQNEILRLA 502 + + TQ +++ A Sbjct: 483 LKANLINHNLTQEQVMEAA 501 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: 602 Number of extensions: 20 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: 513 Length adjustment: 34 Effective length of query: 472 Effective length of database: 479 Effective search space: 226088 Effective search space used: 226088 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