Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter
Query= SwissProt::P37388 (513 letters) >FitnessBrowser__BFirm:BPHYT_RS32815 Length = 519 Score = 556 bits (1432), Expect = e-163 Identities = 286/502 (56%), Positives = 371/502 (73%), Gaps = 3/502 (0%) Query: 4 LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 L+ M+ I K F VKA+D + L + GE V LCGENG+GKSTLMKVL G+YP G+++GEI Sbjct: 5 LMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEI 64 Query: 64 IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEIT-HNGIMDYDLMTLR 122 I+ GE ++A+ +RDTER GI IIHQEL LV EL+V ENIFLGNEIT G M+Y M R Sbjct: 65 IWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMYQR 124 Query: 123 CQKLLAQVSLS-ISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSIL 181 +LL ++ +S I+ V + G G QQL+EIAKALNK+ +LLILDEP++SLT E IL Sbjct: 125 ADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRIL 184 Query: 182 LDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGR 241 LDI+RDL++ G+AC+YISHKL+EV A+ DTI VIRDG+H+ T ++ D II++MVGR Sbjct: 185 LDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGR 244 Query: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301 E+ L+P EPH GD I H+T + N KRVNDVSF L+ GEILG+AGLVGAGRT Sbjct: 245 EIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGLVGAGRT 304 Query: 302 ETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNI 361 E +Q +FG +PG E + +DGK + IR AI GI MVPEDRKR GIVP ++VG NI Sbjct: 305 ELMQAIFGAYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPGLSVGHNI 364 Query: 362 TLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLL 421 TLA L +F G ++D AAE I +++L V+ + P L+I LSGGNQQKA+L R LL Sbjct: 365 TLAVLQRFASG-GRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAVLTRMLL 423 Query: 422 LNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEG 481 NP++LILDEPTRG+D+GAKYEIYKLI QL Q+G++++++SSELPEVLG+SDRVLV+ EG Sbjct: 424 TNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVLVIGEG 483 Query: 482 KLKANLINHNLTQEQVMEAALR 503 +L+ + +N LTQE ++ AA+R Sbjct: 484 ELRGDFVNDGLTQEDILSAAIR 505 Score = 88.6 bits (218), Expect = 5e-22 Identities = 58/233 (24%), Positives = 121/233 (51%), Gaps = 6/233 (2%) Query: 274 IKRVNDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWP-GQWEGKIYIDGKQVDIRNCQ 332 +K ++ + ++ GE +G+ G GAG++ ++ L GV+P G W+G+I +G+ + + + Sbjct: 18 VKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTWDGEIIWEGEPLKAASVR 77 Query: 333 QAIAQGIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGGISQLDDAAEQKCILESIQQL 392 GI ++ ++ +VP ++V +NI L GG +++ AA + E +++L Sbjct: 78 DTERAGIIIIHQELM---LVPELSVAENIFLGNEITLPGG--RMNYAAMYQRADELLREL 132 Query: 393 KVKTSSPDLAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLV 452 + + + GG+QQ +A+ L ++LILDEP+ + + ++ L Sbjct: 133 GISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSEIRILLDIVRDLK 192 Query: 453 QQGIAVIVISSELPEVLGLSDRVLVMHEGKLKANLINHNLTQEQVMEAALRSE 505 ++G+A + IS +L EV + D + V+ +G+ A LT ++++ + E Sbjct: 193 RRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMRALTTDRIISLMVGRE 245 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: 753 Number of extensions: 25 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 519 Length adjustment: 35 Effective length of query: 478 Effective length of database: 484 Effective search space: 231352 Effective search space used: 231352 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