Align ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 162 bits (410), Expect = 9e-45 Identities = 94/287 (32%), Positives = 156/287 (54%), Gaps = 13/287 (4%) Query: 31 LFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGSSWSGILVDP 90 LF+ P ++ L + +PL W TD + G G+FIG N+ + G S + + Sbjct: 15 LFMAPAVILLVVFLTYPLGLGIWLGFTDTKIG--GEGSFIGLDNFTYLAGDSLAQL---- 68 Query: 91 QWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAIPTIVSAKIW 150 ++ NT+++TV + L+ +LGL +A+LLN + RA++L+PW +PT +SA + Sbjct: 69 ----SLFNTVFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALSALAF 124 Query: 151 SWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLAALQM 210 W+ + QF +I+ + +GLID + + D + W+ + +VW+ +PFV + +LA LQ Sbjct: 125 WWLYDAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQT 184 Query: 211 LPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSNS--S 268 + YEAA +DG P + F VTLPLL P + V F +L + F +IYVLT + Sbjct: 185 ISPSLYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGGPLN 244 Query: 269 STMSMSVYARQHLVEFQDVGYGSAASTLLF-LVVAVIALLYLYLGRR 314 +T M+ + Q + +G G+A +T + ++A I Y L RR Sbjct: 245 ATHLMATLSFQRAIPGGALGEGAALATYMIPFLLAAIMFSYFGLQRR 291 Lambda K H 0.329 0.140 0.443 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: 271 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: 320 Length of database: 299 Length adjustment: 27 Effective length of query: 293 Effective length of database: 272 Effective search space: 79696 Effective search space used: 79696 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