Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SMc02031 SMc02031 permease
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 240 bits (612), Expect = 4e-68 Identities = 143/344 (41%), Positives = 196/344 (56%), Gaps = 28/344 (8%) Query: 13 VPPGARRSSSTTAQWLLHRLGMLPVLVVL--YLLFYGLTLYLSGDGTSNFASAENTMNIL 70 +P G + T + ++ + G L LV+L YL F TSNF + +N N+ Sbjct: 11 IPAGGAGARKTKLKAVVFQAGPLIALVLLMAYLAF----------ATSNFLTLDNLSNVA 60 Query: 71 RQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSA----VLGMQ------VSLG-AAPGWA 119 RQ A +LA G TFVILT GIDLSV ++ A+SA VL Q + G P A Sbjct: 61 RQSAFVAILAVGQTFVILTGGIDLSVAAIAALSASITAVLLTQPLVLFGIDFGFVPPPVA 120 Query: 120 IPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTV----LNNDIP 175 I + I G+ G +NG +++ I F+ TLGTMTAFRGAA L+ DG V +P Sbjct: 121 ILIGILIGMAAGALNGWLISKFKIPDFIATLGTMTAFRGAALLVTDGLPVPSFNAGRQLP 180 Query: 176 -SFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGL 234 S W+G G VP +A+ W +LR T LG IYA+GGN AA +GI + Sbjct: 181 ESLIWVGGGQLFGVPVSALIALLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISR 240 Query: 235 VLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGT 294 + Y+ISGL + +AG + RL AN G EL +IA+VV+GGT+L GG G +WG+ Sbjct: 241 TKIMTYAISGLLAAIAGIILVGRLNSANALMADGEELRSIASVVIGGTNLFGGEGGVWGS 300 Query: 295 VVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 ++GA IIGV+ NGL +L +S FWQ +A+G VIV+ VI D+WR++ Sbjct: 301 IIGAAIIGVLGNGLNLLDVSPFWQRIAQGVVIVVVVIFDQWRRR 344 Lambda K H 0.324 0.138 0.417 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: 326 Number of extensions: 20 Number of successful extensions: 3 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: 344 Length of database: 349 Length adjustment: 29 Effective length of query: 315 Effective length of database: 320 Effective search space: 100800 Effective search space used: 100800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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