Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate SMc00139 SMc00139 amino acid ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Smeli:SMc00139 Length = 267 Score = 161 bits (407), Expect = 1e-44 Identities = 84/215 (39%), Positives = 127/215 (59%), Gaps = 1/215 (0%) Query: 9 GYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLV 68 G+G +A G +T LA L + L +G A AK S K LR+ +YTT+ R +P+L+ Sbjct: 44 GWGDEIAYGFLVTASLAVATLPVGLVIGFFVALAKQSEEKSLRLAGNIYTTIFRGLPELL 103 Query: 69 LILLIFYSLQLWLNDLSEVFGWD-YFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVG 127 + +++Y LQ+ + G++ EI+ F AG+I LG ++ AY +E A ++P G Sbjct: 104 TLFIVYYGLQILVQQFLATVGYEGAVEINAFVAGMIALGVVFSAYCSEVLLSAFKAIPHG 163 Query: 128 QLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQN 187 Q EA A GL R + L++ PQL+R ALPGLGN W+ LLK TALVS+IGL D+++ Sbjct: 164 QYEAGDALGLHRGKTMRLIILPQLIRIALPGLGNLWMALLKDTALVSVIGLPDILRQTGI 223 Query: 188 AGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLER 222 A + T F +A +++LV+ +S+ V LER Sbjct: 224 AARVTKHAFEFFGIACVLFLVLAMISSVVFSALER 258 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: 162 Number of extensions: 8 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: 267 Length adjustment: 24 Effective length of query: 209 Effective length of database: 243 Effective search space: 50787 Effective search space used: 50787 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