Align ABC transporter for L-Histidine, permease component (characterized)
to candidate Ac3H11_458 Phosphate transport system permease protein PstA (TC 3.A.1.7.1)
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_458 Length = 284 Score = 52.0 bits (123), Expect = 1e-11 Identities = 46/145 (31%), Positives = 65/145 (44%), Gaps = 18/145 (12%) Query: 76 IVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQ 135 IVG L +VG +LV+T I VL G+ L S +S + + + DIM Sbjct: 71 IVGSLMMVGFT------------VLVSTPIGVLAGVYLAEYSGQS-KTAELTRFVTDIML 117 Query: 136 TMPS-----FVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINA 190 + PS FVY I V + A + A P ++R T+ +R V G + EA A Sbjct: 118 SAPSIVLGLFVYAIAVATVGNFSGWAGSLALSLIAVPVVVRTTENMLRLVPGSLREAAFA 177 Query: 191 FGANRWQQLFGVQLPLALPSIMAGI 215 GA RW+ V L A +M G+ Sbjct: 178 LGAPRWKVSTMVTLRAARSGVMTGL 202 Lambda K H 0.328 0.142 0.429 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: 193 Number of extensions: 13 Number of successful extensions: 1 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: 283 Length of database: 284 Length adjustment: 26 Effective length of query: 257 Effective length of database: 258 Effective search space: 66306 Effective search space used: 66306 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 (21.7 bits) S2: 47 (22.7 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