Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate AZOBR_RS25220 AZOBR_RS25220 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__azobra:AZOBR_RS25220 Length = 252 Score = 150 bits (378), Expect = 3e-41 Identities = 85/246 (34%), Positives = 136/246 (55%), Gaps = 6/246 (2%) Query: 6 RWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMTIWRV 65 R L +A V +A W G++ P L P + K L + +G+++ RV Sbjct: 3 RAALYVALPVALLAAWQAAFALGYIRPILLPPPTRVGKAFVDLAASGDLFRHLGVSLLRV 62 Query: 66 VGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKIL 125 + GF +AA++ +PLGI +G + ++ + I + +P A+IPL ILW GIGEA K+ Sbjct: 63 LEGFAIAALVGLPLGIGIGLSRTLDRLTDLIIQLTKPIPPIAWIPLAILWFGIGEAGKVY 122 Query: 126 VIFIGSVFQITLMVAVTVGGARRD---LVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLR 182 +IF+G++F I + T+ G R+ VE A L + + +V++PGA P I LR Sbjct: 123 IIFLGAIFPI---LVNTIDGNRQTDHRHVELARVLEVTRRRFILQVVLPGALPNIMTGLR 179 Query: 183 LVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALN 242 + L AW V+ AELI +SSG+G++I D++ + T Q++ G+I IG +G + D +A Sbjct: 180 VGLMVAWICVVAAELIAASSGLGYLIMDARQMSQTDQVLVGMITIGAMGKLLDVVLRAAE 239 Query: 243 HRLFAW 248 RL W Sbjct: 240 RRLITW 245 Lambda K H 0.331 0.145 0.456 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: 161 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: 252 Length of database: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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