Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Dino:3608832 Length = 268 Score = 84.3 bits (207), Expect = 2e-21 Identities = 71/224 (31%), Positives = 97/224 (43%), Gaps = 25/224 (11%) Query: 13 MLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILL 72 ++ G + AL L A K S LRVPA + + R P L + Sbjct: 35 LIGSGLIWNVYFGAFALLFGFFLATAVALGKASDRAVLRVPADWFIFVFRGSP-LFIQFF 93 Query: 73 IFYSLQLWLNDLSEVFGWDYFEIDPFT---AGVITLGFIY-GAYFTENFRGAILSVPVGQ 128 + Y L + L +S F DPFT AG + + F+ AY E F GA+ SVP G Sbjct: 94 LAYFLFIQLKAVSPAF-------DPFTSAWAGALVVLFLNTSAYAGEIFYGALRSVPKGD 146 Query: 129 LEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGL------SDLV 182 LEAA AYGL+ W +F V +P ++R A P N + L +T LV G D + Sbjct: 147 LEAADAYGLAGWTKFRRVTWPTMLRLAWPSYTNEAIFLFHATTLVFFAGFPAFQQRGDAL 206 Query: 183 KAAQNAGKTTNEPL-------YFLILAGLMYLVITTLSNRVLKR 219 AQ T P ++ IL L + + +L NR L R Sbjct: 207 YYAQYFADKTFNPFIPYPIVAFYFILLTLAVIFVFSLINRRLNR 250 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: 170 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: 233 Length of database: 268 Length adjustment: 24 Effective length of query: 209 Effective length of database: 244 Effective search space: 50996 Effective search space used: 50996 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