Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_013403235.1 CALHY_RS06825 branched-chain amino acid ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >NCBI__GCF_000166355.1:WP_013403235.1 Length = 294 Score = 276 bits (706), Expect = 4e-79 Identities = 141/302 (46%), Positives = 208/302 (68%), Gaps = 9/302 (2%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60 M F+QQLING++LG++Y LI++GYTMVYGII +INFAHG+I+M+GA++A L Sbjct: 1 MSTFIQQLINGITLGSVYALISLGYTMVYGIIKLINFAHGDIFMVGAYIAY--------L 52 Query: 61 GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120 +T++ L L+ L+ SM+F ++ G +E+ AY+PLR+SPR++ LI+AIG+S+ L+N +QI Sbjct: 53 SVTYLKLGLIPSLIVSMVFCSILGMLIEKFAYKPLRNSPRISALITAIGVSLLLENLMQI 112 Query: 121 LQGARSKPLQPILPG-NLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179 + GA S+ ++ N L + V+ ++ ++IT+ LM ++ +T +G+A RA Sbjct: 113 IMGADSRVFPRLVAEKNYHLFQDRIVVNNKQIYLLIITVLLMIILNFVVKKTKIGKAMRA 172 Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239 QD A L+G+NVD IS TF +G+ALAA AG++V L Y I+ +G L G+KAF AA Sbjct: 173 VSQDMDAARLMGINVDTTISYTFAIGSALAAAAGVLVGLYYNTINPLMGVLPGLKAFIAA 232 Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299 V GGIG +PGAMLGG +G+IE SGY S +KD F +L+L+LI +P+GLLG+ E Sbjct: 233 VFGGIGIIPGAMLGGFSLGIIETLVSGYGSSMYKDAVAFALLILILIIKPSGLLGKNIKE 292 Query: 300 KV 301 KV Sbjct: 293 KV 294 Lambda K H 0.329 0.144 0.425 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: 337 Number of extensions: 20 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: 301 Length of database: 294 Length adjustment: 26 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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 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