Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__HerbieS:HSERO_RS01335 Length = 283 Score = 117 bits (292), Expect = 5e-31 Identities = 73/234 (31%), Positives = 119/234 (50%), Gaps = 7/234 (2%) Query: 153 PPEFTFA-NYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGR 211 P +F NY L + M F+N+ +TIP+ I I +AA A +AL+ +F G Sbjct: 55 PQDFAMLENYREAL----TASPMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGN 110 Query: 212 ALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVG 271 +L A V VP Q+ +IP+ L ++G+ G L H LRN++ Sbjct: 111 TVLFATFVACNFVPQQILMIPVRDLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQ 170 Query: 272 LPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQ 331 LP ++IE A+++GA+++ +F +IVLPL PALA+ A+ F + WND A V + Sbjct: 171 LPFEMIEAARIEGASEWTVFYRIVLPLIRPALAALAVLVFTFVWNDYFWALV--LTQGDD 228 Query: 332 TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 +T + L G W +++ + ++ +++FF MQ+ V GL G+ K Sbjct: 229 VAPITVGVAALRGQWTTAWNLVSAGSILAALPSVILFFVMQKQFVAGLTFGASK 282 Lambda K H 0.323 0.138 0.419 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: 268 Number of extensions: 14 Number of successful extensions: 2 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: 385 Length of database: 283 Length adjustment: 28 Effective length of query: 357 Effective length of database: 255 Effective search space: 91035 Effective search space used: 91035 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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