Align Arginine ABC transporter permease protein ArtM (characterized)
to candidate WP_061534652.1 CAter10_RS19015 amino acid ABC transporter permease
Query= SwissProt::P0AE30 (222 letters) >NCBI__GCF_001584165.1:WP_061534652.1 Length = 250 Score = 92.8 bits (229), Expect = 5e-24 Identities = 63/216 (29%), Positives = 115/216 (53%), Gaps = 3/216 (1%) Query: 4 YLPELMKGLHTSLTLTVASLIVALILALIFTIILTLKTPVLVWLVRGYITLFTGTPLLVQ 63 Y+ L+ GL +L L++++ I+ALI+ + I T+ V + GY+ LF PL+VQ Sbjct: 21 YMDTLLAGLKWTLALSISAWIMALIIGTVIGTIRTMPNKWAVRVANGYVELFRNIPLIVQ 80 Query: 64 IFLIYYGPGQFPTLQEYPALWHLLSEPWLCALIALSLNSAAYTTQLFYGAIRAIPEGQWQ 123 +FL Y+ + L L + ++ A +AL +++ I A+P GQ Sbjct: 81 MFLWYFVMPEIVPAGIGNWLKSLPNASFVTAFLALGFFTSSRIAVQVSAGINALPRGQKL 140 Query: 124 SCSALGMSKKDTLA-ILLPYAFKRSLSSYSNEVVLVFKSTSLAYTITLMEVMGYSQLLYG 182 + +ALG++ T +LLP +F+ + S +NE + K++S+A TI L+E+ + + Sbjct: 141 AGTALGLTLPQTYRYVLLPMSFRIIIPSLTNEFAAIIKNSSVALTIGLVELTAATYSMRE 200 Query: 183 RTYDVM-VFGAAGIIYLVVNGLLTLMMRLIERKALA 217 T+ A +IY++++G+ L+ R +E KA+A Sbjct: 201 FTFQTFESLTGATVIYVIISGIALLLARWLE-KAIA 235 Lambda K H 0.328 0.140 0.418 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: 130 Number of extensions: 9 Number of successful extensions: 3 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: 222 Length of database: 250 Length adjustment: 23 Effective length of query: 199 Effective length of database: 227 Effective search space: 45173 Effective search space used: 45173 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