Align arginine/ornithine transport protein (characterized)
to candidate WP_054656298.1 CES79_RS03760 amino acid ABC transporter permease
Query= CharProtDB::CH_107317 (229 letters) >NCBI__GCF_002217945.1:WP_054656298.1 Length = 247 Score = 105 bits (263), Expect = 6e-28 Identities = 70/203 (34%), Positives = 110/203 (54%), Gaps = 9/203 (4%) Query: 15 LTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAWCGDLYATVVRGIPDLVLILLIFYGGQG 74 +TL +A+LSM+LAI +G + +LS + L Y ++ RG+P LV + +IFYG Sbjct: 21 ITLLMAILSMILAIFIGGFLTSLQLSTIAPLRGFAHFYISLFRGMPTLVQLFIIFYG--- 77 Query: 75 LLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGEAGYGYGMS 134 PQ+ + L+ FV+ V LGF +YL+E FR A ++ KGQ EAG +S Sbjct: 78 -----LPQI-FPALRGLSAFVAVVVGLGFKQASYLAEIFRAAVNSVDKGQIEAGQSLNIS 131 Query: 135 HRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASDATREPFTY 194 ++F + +PQ A+P N ++ LVK T+L +GL ++ K + + + F Sbjct: 132 RTKLFLNVVLPQATINALPATGNTFVSLVKETSLAFTLGLTELFGDGKLIAGQSFKYFET 191 Query: 195 YLAVAGLYLLVTSVSLLLLRLLE 217 YLAV +Y L+ ++ L LLE Sbjct: 192 YLAVGIIYWLLITIYTWLQHLLE 214 Lambda K H 0.328 0.144 0.442 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: 129 Number of extensions: 7 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: 229 Length of database: 247 Length adjustment: 23 Effective length of query: 206 Effective length of database: 224 Effective search space: 46144 Effective search space used: 46144 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 24 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