Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Marino:GFF3090 Length = 240 Score = 105 bits (261), Expect = 1e-27 Identities = 62/205 (30%), Positives = 103/205 (50%), Gaps = 2/205 (0%) Query: 17 GAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILLIFYS 76 G T+ L FL+L + L + + A + ++ P LYT L R P L+ + +I+Y Sbjct: 26 GMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVSGPVWLYTYLFRGTPLLIQLYIIYYG 85 Query: 77 LQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLEAATAYG 136 L + + E F W+ F +PF ++ AY TE RGAI+S P G++EAA AYG Sbjct: 86 LAQ-IEGIQETFWWEIFR-EPFYPALLAFTLNTAAYTTEIIRGAIISTPNGEIEAAKAYG 143 Query: 137 LSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAGKTTNEPL 196 ++ + R ++ P R A+ N + +L ++A+ S++ + DL AA+N P Sbjct: 144 MNWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIASVVTIVDLTGAARNIYSRFYAPF 203 Query: 197 YFLILAGLMYLVITTLSNRVLKRLE 221 I L Y+ +T + ++LE Sbjct: 204 DAFIFVALCYMALTFILVFAFRKLE 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: 143 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: 233 Length of database: 240 Length adjustment: 23 Effective length of query: 210 Effective length of database: 217 Effective search space: 45570 Effective search space used: 45570 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