Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__Koxy:BWI76_RS27035 Length = 513 Score = 894 bits (2309), Expect = 0.0 Identities = 451/513 (87%), Positives = 485/513 (94%) Query: 1 MPYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYE 60 M +LLEMKNITKTFG+VKAIDNV LRLNAGE+VSLCGENGSGKSTLMKVLCGIYPHGSYE Sbjct: 1 MSWLLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYE 60 Query: 61 GEIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMT 120 GEIIF+GE +Q HIRDTERKGIAIIHQELALVK LTVLENIFLG EI+ +G++DY+ MT Sbjct: 61 GEIIFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMT 120 Query: 121 LRCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSI 180 LRC+KLLAQV+L+ISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQET+I Sbjct: 121 LRCEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAI 180 Query: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVG 240 LL+IIRDLQ HGIACIYISHKLNEVKAISDTICVIRDGQHIGTR+A GMSEDDIITMMVG Sbjct: 181 LLNIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVG 240 Query: 241 RELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGR 300 RELTALYP+E H+ GDEILR+E+LTAWHPVNRHIKRVNDVSFSL+RGEILGIAGLVGAGR Sbjct: 241 RELTALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGR 300 Query: 301 TETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 TE +QCLFGVWPG+W+GKI+IDG+ V I CQQAIAQGIAMVPEDRK+DGIVPVMAVGKN Sbjct: 301 TEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKN 360 Query: 361 ITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCL 420 ITLAALN+FTG +S LDDA EQ CI +SIQ+LK+KTSSP+LAIGRLSGGNQQKAILARCL Sbjct: 361 ITLAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAILARCL 420 Query: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE Sbjct: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480 Query: 481 GKLKANLINHNLTQEQVMEAALRSEHHVEKQSV 513 GKLKANLIN LTQEQVMEAALRSE HVE+ V Sbjct: 481 GKLKANLINQGLTQEQVMEAALRSERHVEEHVV 513 Lambda K H 0.319 0.137 0.391 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: 999 Number of extensions: 36 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: 513 Length of database: 513 Length adjustment: 35 Effective length of query: 478 Effective length of database: 478 Effective search space: 228484 Effective search space used: 228484 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 (21.8 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