Align ABC transporter permease (characterized, see rationale)
to candidate WP_004323278.1 C665_RS16640 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000310185.1:WP_004323278.1 Length = 296 Score = 153 bits (387), Expect = 4e-42 Identities = 94/305 (30%), Positives = 159/305 (52%), Gaps = 19/305 (6%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 L + ++ GL G +YAL L + M+Y +++N A GE+LMIGA + C G+ Sbjct: 10 LAEIMLAGLGAGGLYALTGLAFVMIYKATRVVNLAIGEMLMIGA---YLCFGLATAM--N 64 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 P W LA ++A + + ++E+VA RP+ +A + +G++ +L + +IW Sbjct: 65 LPMW----LAILVAVIGSGGAGALLERVAIRPMLGESPIAVFMVTVGLASILVGVVELIW 120 Query: 124 KPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAEN 183 + P +P++P IG AF+ V AV + + + G A+RATA + Sbjct: 121 TSEPRRLPEFMPATPVMIGEAFVPSKVFYGFLVAAVLIGVALAVFRFWRGGVALRATASD 180 Query: 184 PRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGG 243 + A MG+ V S ++ + A++AAIAG++ + G TMG GL + GG Sbjct: 181 QQAAYSMGIDVPKVFSLSWTVAAMIAAIAGVIVGA-VGGISSTMGVF-GLSVLVVVIVGG 238 Query: 244 IGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGE 303 + ++ GA+V G+L+G++E +L GG LG Y + F++LI++L +RP GL G Sbjct: 239 LDSVLGALVAGLLIGVVE--------SLAGGFLGGEYKLLATFLILIVVLLVRPYGLFGT 290 Query: 304 RVADR 308 +R Sbjct: 291 HEIER 295 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: 231 Number of extensions: 16 Number of successful extensions: 4 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: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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 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