Align Inner-membrane translocator (characterized, see rationale)
to candidate SM_b21342 SM_b21342 sugar uptake ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Smeli:SM_b21342 Length = 332 Score = 161 bits (408), Expect = 2e-44 Identities = 107/310 (34%), Positives = 164/310 (52%), Gaps = 17/310 (5%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 L + L G +++ F S + + LR N+ + ALGM VI++GGIDLSVG A++ V Sbjct: 27 LFGLILFGALRYENFLSQYNILSFLRYNSMFALIALGMAFVIMTGGIDLSVGGTAAMASV 86 Query: 76 VTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTL 135 V +LL + Y W L + G GAL G + V ++QPFI TLA M A G L Sbjct: 87 VAALL-SPYHWAAGLFGGIAA--GFAVGALNGFTVTVMRIQPFIATLATMLAAYGTGLLL 143 Query: 136 SEE---SIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYA 192 + S++ D F + + P + + I +L +V +V+ G +V A Sbjct: 144 AGNQSVSVSYDSGFTSIGQDDFLGFP------IPAWIALLVYVAGWLVLERLPVGRHVLA 197 Query: 193 IGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAV 252 IG + +A LMG+ + +T ++Y S LA LAG++ +G +G EL AIA+V Sbjct: 198 IGDGEATAALMGLKVRRTLAAVYVGSGALAGLAGVILASQFGAGQPTEGVGWELFAIASV 257 Query: 253 VIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDG-----SLSSWWTKIVIGLLLFFFIL 307 V+GGTLLTGGSG V T+ G +L+ ++ + F+ SLS++W ++ G L ++ Sbjct: 258 VVGGTLLTGGSGSVGATLAGALLLAMVFNILNFENGLGWISLSAYWQSVIRGGFLLIVVV 317 Query: 308 LQKLLNGRKT 317 LQ L R+T Sbjct: 318 LQARLMSRRT 327 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: 319 Number of extensions: 22 Number of successful extensions: 5 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