Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate BPHYT_RS25965 BPHYT_RS25965 nitrate ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__BFirm:BPHYT_RS25965 Length = 323 Score = 158 bits (400), Expect = 1e-43 Identities = 90/226 (39%), Positives = 127/226 (56%), Gaps = 7/226 (3%) Query: 30 VSPTFLASPITMAKEGWLLFTEYGFIKD---IGMTIWR----VVGGFVLAAVIAVPLGIA 82 V+P +L +P + + + F +D + ++W + GFVL++VI VP+GI Sbjct: 92 VNPVYLPAPHEVLRAFYTAFATPPASRDGVWLHQSLWHSIQVIFWGFVLSSVIGVPIGIV 151 Query: 83 MGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEAQKILVIFIGSVFQITLMVAVT 142 G Y I EPF F RYLPA AF L++ GI + KI +I IG++FQ L+VA T Sbjct: 152 CGTYSAIARLQEPFFEFFRYLPAPAFGALMVAILGIYDGPKIAIIVIGTLFQQVLIVANT 211 Query: 143 VGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETLRLVLGWAWTYVIVAELIGSSS 202 L EAA TLG ++T V+IPG P++ R++LGWAWTY+IVAEL+G+SS Sbjct: 212 TRKLEYGLFEAAMTLGTKKLKLLTHVVIPGILPDLYRDQRILLGWAWTYLIVAELVGTSS 271 Query: 203 GIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKALNHRLFAW 248 GI IT + + I++IG+IGL +D L RLF W Sbjct: 272 GITWYITQQARYEHFDNVYAAIMMIGIIGLGTDLVLAYLGRRLFPW 317 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: 243 Number of extensions: 9 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: 252 Length of database: 323 Length adjustment: 26 Effective length of query: 226 Effective length of database: 297 Effective search space: 67122 Effective search space used: 67122 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: 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