Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Koxy:BWI76_RS27035 Length = 513 Score = 388 bits (997), Expect = e-112 Identities = 208/499 (41%), Positives = 314/499 (62%), Gaps = 8/499 (1%) Query: 12 YLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GS 69 +LLEM+ I K+F VKA+DNV+L + + +L GENG+GKSTL+K L GIY S G Sbjct: 3 WLLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62 Query: 70 IVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQD 129 I+F G+ + ++ GI+++HQEL LV +V++N++LG ++ +D + M Sbjct: 63 IIFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLR 122 Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189 + + ++++ I P RVG L + Q Q++EIAKA + +++I+DEPT+SLTE+E L Sbjct: 123 CEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILL 182 Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRS 249 IIR L+ G +YISHK+ E+ + D I ++RDGQ I T+ +G+ D II MMVGR Sbjct: 183 NIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGRE 242 Query: 250 LNQRFPDKENKPGDVILEVRHLTSLRQPS-----IRDVSFDLHKGEILGIAGLVGAKRTD 304 L +P + + GD IL V +LT+ + + DVSF L +GEILGIAGLVGA RT+ Sbjct: 243 LTALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGRTE 302 Query: 305 IVETLFGI-REKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSL 363 V+ LFG+ + G I + G+ + HT +AI G A+V E+R+ GI + +G N Sbjct: 303 AVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKNIT 362 Query: 364 ISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLT 423 ++ + + + LD++ + Q I +++KT IG LSGGNQQK I+ R LL Sbjct: 363 LAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAILARCLLL 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 LKANLINQGLTQEQVMEAA 501 Lambda K H 0.319 0.137 0.388 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: 612 Number of extensions: 22 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: 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 ( 7.4 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