Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_092348288.1 BLU87_RS11125 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >NCBI__GCF_900107645.1:WP_092348288.1 Length = 317 Score = 119 bits (299), Expect = 5e-32 Identities = 74/214 (34%), Positives = 116/214 (54%), Gaps = 11/214 (5%) Query: 9 WEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPML 68 W+A PL + GL TL + AL+ GL+ + GL RVSK + + + +IRGTP+L Sbjct: 110 WKAGPL-VTGLWVTLWISALASIIGLVIGVVTGLCRVSKNLTLRQLSITYIELIRGTPLL 168 Query: 69 VQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEI 128 VQLF+ Y+ L + L+S F A AI AY AEII +++ P G++ Sbjct: 169 VQLFIFYFFLGTVLDIGR------LASGIF----ALAIFAGAYVAEIIRAGIQSIPKGQM 218 Query: 129 EAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVN 188 EAA+++GM+ + I+LP A +R LP + + I +++ +SL S++ + D+T + R V Sbjct: 219 EAARSLGMNVPQAMIYIILPQAFKRTLPPLAGQFISLIKDSSLVSVIAITDLTKSGREVI 278 Query: 189 AQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHR 222 + FE + YL LTF L ++ E R Sbjct: 279 TSTFAVFEIWFVVAFLYLILTFSLSQVVAWVERR 312 Lambda K H 0.330 0.140 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: 172 Number of extensions: 6 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: 317 Length adjustment: 25 Effective length of query: 207 Effective length of database: 292 Effective search space: 60444 Effective search space used: 60444 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 (21.9 bits) S2: 47 (22.7 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