Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b20929 SM_b20929 sugar uptake ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Smeli:SM_b20929 Length = 332 Score = 158 bits (400), Expect = 2e-43 Identities = 98/314 (31%), Positives = 174/314 (55%), Gaps = 13/314 (4%) Query: 10 WITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAV 69 W+ +++L + + D FA+ + + N+ R+ F+ I ALGMTLVII+GGIDLSVG+V Sbjct: 27 WVLVAVILACLFL-SIATDSFATAKNLYNITRNFTFVAIIALGMTLVIITGGIDLSVGSV 85 Query: 70 IALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLAR 129 + L +V ++++ + + + + GA G +I PF++TL + +AR Sbjct: 86 LCLCSMVLAVVM-HAGYGIEVGIAASIGTALVAGAFNGVMIAYLGFPPFVITLGMLSIAR 144 Query: 130 GLATTLSEESIAIDH-PFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAV----VMHYT 184 LA S ++ + P +D + + G GA L +L+ +++A+ V+ +T Sbjct: 145 SLAMVASNNTVVFEFGPDHDTLLAL-----GGGAWFLGIANPVLYMIVLALLTGFVLRWT 199 Query: 185 RFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGV 244 +FG V+AIGGN+H+A L G+ + + +++Y IS+ A +AGI+ T + + G+ Sbjct: 200 KFGRYVFAIGGNEHAATLTGVPVRRIKVAVYMISALAAGIAGIIQTGWLGAVTTNIGAGM 259 Query: 245 ELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFF 304 EL IAA VIGG L GG+G G ++G L+ VI+ + G ++++W IG + Sbjct: 260 ELQVIAAAVIGGANLAGGAGTASGALIGAALIEVIRNSLGLLG-INAFWQGAFIGGAIVL 318 Query: 305 FILLQKLLNGRKTQ 318 +L ++ N R+++ Sbjct: 319 AVLFDRIRNFRQSE 332 Lambda K H 0.330 0.145 0.424 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: 345 Number of extensions: 26 Number of successful extensions: 4 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: 320 Length of database: 332 Length adjustment: 28 Effective length of query: 292 Effective length of database: 304 Effective search space: 88768 Effective search space used: 88768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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