Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate BWI76_RS09505 BWI76_RS09505 arginine transporter permease subunit ArtM
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__Koxy:BWI76_RS09505 Length = 222 Score = 141 bits (356), Expect = 9e-39 Identities = 79/216 (36%), Positives = 132/216 (61%), Gaps = 3/216 (1%) Query: 12 LPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQL 71 LP GL T+L L A S++ L+ +L ++ K P++ Y + GTP+LVQ+ Sbjct: 5 LPELLKGLHTSLTLTAASIVVALILSLIFTIILTLKTPVLVWIVRGYITLFTGTPLLVQI 64 Query: 72 FLIYYGLAQFEAVRE-SFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEA 130 FLIYYG QF +++E LW +S CA +A ++N++AYT ++ G++RA P+G+ ++ Sbjct: 65 FLIYYGPGQFPSLQEYPVLWHLISEPWLCALIALSLNSAAYTTQLFHGAIRAIPDGQWQS 124 Query: 131 AKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQ 190 A+GMS+ K ILLP A +RAL YSNEV+++ ++TSLA +TL+++ G ++ + + Sbjct: 125 CGALGMSK-KDTLAILLPYAFKRALSSYSNEVVLVFKSTSLAYTITLMEVMGHSQLLYGR 183 Query: 191 YYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGY 226 Y + AG+ YL + +L L ++ EH+ L + Sbjct: 184 TY-DVMVFGAAGIVYLVVNGLLTLLMRLIEHKALAF 218 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: 138 Number of extensions: 11 Number of successful extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 210 Effective length of database: 200 Effective search space: 42000 Effective search space used: 42000 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