Align ABC transporter for L-Histidine, permease component (characterized)
to candidate AO353_22195 AO353_22195 metal ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22195 Length = 223 Score = 76.3 bits (186), Expect = 6e-19 Identities = 62/210 (29%), Positives = 107/210 (50%), Gaps = 27/210 (12%) Query: 89 WDKLMQ--------TLALMLVATLISVLIGIPLGILSARSN--------RLRSVLMPLLD 132 W++++Q TL ++L+A ++LIG+PLG+L S +L L L++ Sbjct: 7 WNEILQLVLNATGETLYMVLLAGFFTLLIGLPLGVLLFISRSGGLYPMPKLNKGLGGLVN 66 Query: 133 IMQTMPSFVYLIPVLMLFGL------GKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVME 186 + +++P V LI ++ L L G A+ I A P R+ + + +VD +E Sbjct: 67 LGRSLPFVVMLIALIPLTRLIVGTTLGSTAAVVPITIGAFPFFARIVENALDEVDKGRIE 126 Query: 187 AINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGE-DVLVGI 245 AI A G + +F V LP ALP+++AGI T +M + +A +IG GLG+ + G Sbjct: 127 AILAMGGDIRHVIFKVLLPEALPALLAGITLTLVMLIGFSSMAGVIGGGGLGDLAIRYGY 186 Query: 246 QTLNVGRGLEAGLAIVILAVVIDRITQAYG 275 Q N + +A V++ V++ + Q+ G Sbjct: 187 QRFN----NQVMVATVVVLVILVQGVQSLG 212 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: 162 Number of extensions: 6 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: 283 Length of database: 223 Length adjustment: 24 Effective length of query: 259 Effective length of database: 199 Effective search space: 51541 Effective search space used: 51541 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: 46 (22.3 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