Align ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1939 Length = 291 Score = 154 bits (388), Expect = 3e-42 Identities = 99/307 (32%), Positives = 171/307 (55%), Gaps = 29/307 (9%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 +Q +I+G+ G +Y LIALG+ ++Y + ++FA GE++M+GA + + ++ G Sbjct: 4 VQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVL-----GF 58 Query: 65 PGWVILLLATIIACVVAATL-NFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 P WV ++A VVA L ++E+ RP+ P + ++ IG+ +L+ L +I Sbjct: 59 PFWV-----AVLASVVAMGLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMI- 112 Query: 124 KPNYKPYPTMLP----SSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 PN LP +G ++ Q++++G T L + ++ LG AM+A Sbjct: 113 -PNIGTDTHTLPVPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQA 171 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHT-MGFLPGLKAFTA 238 ++N A MG+ + + + AV+AA+AG++ A T H MGF+ GLKAF A Sbjct: 172 ASQNQLAAYYMGIPVQRLNGLAWGLAAVVAAVAGLLLAPI--TFVHANMGFI-GLKAFPA 228 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 AV GG G+L GA+VGG+++G++E +L+G L + D A+IV++I+L ++P+ Sbjct: 229 AVVGGFGSLPGAIVGGLVIGIVE--------SLSGFYLPDGFKDTAAYIVVLIMLMVKPN 280 Query: 299 GLLGERV 305 GL GE++ Sbjct: 281 GLFGEKL 287 Lambda K H 0.327 0.142 0.419 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: 213 Number of extensions: 12 Number of successful extensions: 5 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: 309 Length of database: 291 Length adjustment: 27 Effective length of query: 282 Effective length of database: 264 Effective search space: 74448 Effective search space used: 74448 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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