Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate HSERO_RS22745 HSERO_RS22745 sugar ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >FitnessBrowser__HerbieS:HSERO_RS22745 Length = 300 Score = 113 bits (283), Expect = 6e-30 Identities = 73/236 (30%), Positives = 127/236 (53%), Gaps = 10/236 (4%) Query: 152 TPPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPG- 210 T TFA ++ +L + F N+L VT+ A + +L A AA+AL F G Sbjct: 73 TAETLTFAGFQKVLAGTH----FLLYFGNSLAVTVAALFLIVLFGAMAAWALTEYRFFGN 128 Query: 211 RALLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMV 270 RAL + +G+++ P++L + +L L A+ + L +T G+PLA+ +L +M Sbjct: 129 RALNFFIAIGIMI-PIRLGTVSILQLVVALDLINTRTALVLVYTAQGLPLAVMILSEFMR 187 Query: 271 GLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATG 330 +P ++ + A+ DG + IF +++LPL PA+A+ A+F + WNDL LI A G Sbjct: 188 QIPGELKDAARCDGVGELSIFFRVILPLLRPAIATVAVFTMIPAWNDLWFP---LILAPG 244 Query: 331 Q-TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385 + T +T + + +G +W + A +++ LL++ + R L+RGL +G+VK Sbjct: 245 EDTRTVTLGVQQFIGQYATDWNSVLAALSMAVIPVLLLYMAFSRQLIRGLTSGAVK 300 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: 248 Number of extensions: 11 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: 300 Length adjustment: 28 Effective length of query: 357 Effective length of database: 272 Effective search space: 97104 Effective search space used: 97104 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