Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate GFF292 PS417_01490 ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__WCS417:GFF292 Length = 231 Score = 186 bits (472), Expect = 3e-52 Identities = 102/228 (44%), Positives = 144/228 (63%), Gaps = 3/228 (1%) Query: 6 NLHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVP 65 +L+G+GP LA GA MT+KLA AL L L LGL A AK S K L+ Y+T++R +P Sbjct: 4 DLYGFGPALAAGALMTVKLALTALCLGLVLGLAGALAKTSPYKPLQWLGGAYSTIVRGIP 63 Query: 66 DLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVP 125 +L+ +LLI++ + L E FG + F AGVI LG +GAY TE FRGAIL++P Sbjct: 64 ELLWVLLIYFGTVNLMRALGEFFGNPDLSLSAFAAGVIALGLCFGAYATEVFRGAILAIP 123 Query: 126 VGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAA 185 G EA A GLS+++ F ++ PQ+ R ALPGLGN +++L+K TALVS+IGL ++++ A Sbjct: 124 KGHREAGIALGLSKFRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHA 183 Query: 186 QNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIKGMAR 233 Q T +P F ++A MYL +T L+ + LE+R +G AR Sbjct: 184 QIGVTVTKQPFTFFMVAAFMYLGLTVLAMTGMHFLEKR---AARGFAR 228 Lambda K H 0.327 0.141 0.428 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: 151 Number of extensions: 6 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: 233 Length of database: 231 Length adjustment: 23 Effective length of query: 210 Effective length of database: 208 Effective search space: 43680 Effective search space used: 43680 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