Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Smeli:SM_b21376 Length = 503 Score = 365 bits (936), Expect = e-105 Identities = 208/497 (41%), Positives = 302/497 (60%), Gaps = 5/497 (1%) Query: 2 ARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAG 61 A +L+ V K++ V AL+ RL +R G VH L G NGAGKST + IL G+ +G Sbjct: 5 AADTILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSG 64 Query: 62 SILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALN 121 I+L+G + P EA + G+A++ QEL +TVAENI REPRR G I D KAL Sbjct: 65 EIVLDGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREPRRFGFIND-KALV 123 Query: 122 RRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQT 181 + ++ L +D T + LS+AQ QLVEIAK SHD +V+I+DEPTS++ + EA+ Sbjct: 124 AKAHRIVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEI 183 Query: 182 LFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241 LF+ I RL +GA I+Y+SHR+ E+ +++DD ++ RDG +V + ++ + L+ +VG Sbjct: 184 LFEIIGRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVG 243 Query: 242 QELTRIDHKVGRECAANTC--LQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFL 299 + + I AA+ L VD L+R GEF D+S +R GEILG +GL+GSGRSE + Sbjct: 244 RRMDEIYPPPVHHVAADRAPVLAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEVM 303 Query: 300 NCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSA 359 N ++G+ A +G+V L G+ + P I G+ VTE+RK+ GLVL S+ NI+++A Sbjct: 304 NALFGMKSA-AGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMAA 362 Query: 360 YKRLS-SWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPV 418 + I E A + V +L IKT SLE P ++SGGNQQK+VLAK L T P Sbjct: 363 LADFAGGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRPK 422 Query: 419 CLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVT 478 L+ DEPTRG+D GAK EIY ++ + G A +++SS+ PE+L +SDR+ V G Sbjct: 423 VLILDEPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPGA 482 Query: 479 ISTDTALSQEALLRLAS 495 +AL+ E ++ A+ Sbjct: 483 TLEGSALTPETIMAHAT 499 Lambda K H 0.319 0.135 0.381 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: 549 Number of extensions: 25 Number of successful extensions: 10 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: 495 Length of database: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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