Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::WCS417:GFF4244 (229 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 60.1 bits (144), Expect = 6e-14 Identities = 37/117 (31%), Positives = 62/117 (52%), Gaps = 2/117 (1%) Query: 101 LGFIFGAYLSETFRGAFMAIPKGQAEAGLAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWL 160 L GA+++E R +A+ KGQ EA A GM ++ +++PQ +R+ IP + +L Sbjct: 286 LALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIPPVISQYL 345 Query: 161 VLTKATALISVVGLQDMM-FKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHL 216 LTK ++L + +G D+ + T F L + YL+I S+S+ AL +L Sbjct: 346 NLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLI-SLSISALMNL 401 Score = 29.3 bits (64), Expect = 1e-04 Identities = 17/53 (32%), Positives = 28/53 (52%) Query: 16 TLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLVLILLI 68 TL +A A + G++ LRLS +A + +Y + R IP L+ I++I Sbjct: 101 TLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIPVLIWIVII 153 Lambda K H 0.329 0.143 0.424 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: 238 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 229 Length of database: 411 Length adjustment: 27 Effective length of query: 202 Effective length of database: 384 Effective search space: 77568 Effective search space used: 77568 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: 48 (23.1 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