Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__Dino:3608832 Length = 268 Score = 113 bits (282), Expect = 4e-30 Identities = 70/229 (30%), Positives = 115/229 (50%), Gaps = 14/229 (6%) Query: 10 EALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLV 69 E L GL+ + A +LLFG A + L + S + ++ + A + +V RG+P+ + Sbjct: 31 EQFTLIGSGLIWNVYFGAFALLFGFFLATAVALGKASDRAVLRVPADWFIFVFRGSPLFI 90 Query: 70 QLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIE 129 Q FL Y+ Q +AV +F +SA A + +NTSAY EI G+LR+ P G++E Sbjct: 91 QFFLAYFLFIQLKAVSPAF--DPFTSAWAGALVVLFLNTSAYAGEIFYGALRSVPKGDLE 148 Query: 130 AAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNA 189 AA A G++ + ++R+ P+ LR A P Y+NE I + T+L V + +A Sbjct: 149 AADAYGLAGWTKFRRVTWPTMLRLAWPSYTNEAIFLFHATTL---VFFAGFPAFQQRGDA 205 Query: 190 QYYL---------PFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAP 229 YY PF Y +++ +T ++ +F + R +LAP Sbjct: 206 LYYAQYFADKTFNPFIPYPIVAFYFILLTLAVIFVFSLINRRLNRHLAP 254 Lambda K H 0.329 0.139 0.427 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: 142 Number of extensions: 5 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: 232 Length of database: 268 Length adjustment: 24 Effective length of query: 208 Effective length of database: 244 Effective search space: 50752 Effective search space used: 50752 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 (21.8 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