Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_086508347.1 BZY95_RS02055 ABC transporter
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_002151265.1:WP_086508347.1 Length = 233 Score = 105 bits (261), Expect = 1e-27 Identities = 68/218 (31%), Positives = 108/218 (49%), Gaps = 7/218 (3%) Query: 13 PLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLF 72 P G TL+L LSL+ L+ L ++S+ +++ A LYT VIRG P LV + Sbjct: 9 PRLLEGAGVTLQLAVLSLILALILGLLTASAKMSRNWLLHKVATLYTTVIRGVPDLVLML 68 Query: 73 LIYYG-----LAQFEAVRESFLWPWLSSATFCAC--LAFAINTSAYTAEIIAGSLRATPN 125 L+++G +A+ + F W + A L AY E G+ A + Sbjct: 69 LLFFGGQMALNVATDAIYDRFGVDWYINLNAFAAGVLTIGFIFGAYMGETFRGAFMAVEH 128 Query: 126 GEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAAR 185 G+IEA KA GMS + +++RI P +R ALP SN +++L+TT+L S++ L D+ A Sbjct: 129 GQIEAGKAYGMSPWLVFRRIRFPQMMRHALPGISNNWMVLLKTTALVSVIGLSDMVRVAA 188 Query: 186 TVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRW 223 + + PF I V YL + + +F + R+ Sbjct: 189 EASRATHEPFTFLIPVAVVYLLIASVSEWMFARLQKRY 226 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: 109 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: 233 Length adjustment: 23 Effective length of query: 209 Effective length of database: 210 Effective search space: 43890 Effective search space used: 43890 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 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