Align ABC transporter permease (characterized, see rationale)
to candidate WP_045585061.1 AL072_RS29560 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_001305595.1:WP_045585061.1 Length = 301 Score = 261 bits (667), Expect = 1e-74 Identities = 142/307 (46%), Positives = 201/307 (65%), Gaps = 18/307 (5%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MD LQQ+INGL LG++Y LIA+GYTMVYGII +INFAHGE+ MIGA + ++ Sbjct: 1 MDYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAF-----VALITFL 55 Query: 61 MPGAPG--WV--ILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQ 116 GA G WV LL+ + + + + + +E++AYRPLRSSPRLAPLI+AIGMSI LQ Sbjct: 56 AIGALGITWVPLALLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115 Query: 117 TLAMIIWKPNYKPYPTMLPSSPFEIGGAF-ITPTQILILGVTAVALASLVYLVNHTNLGR 175 I+ KP +LP + + GA ++ ++ + +T V + L+N T+LGR Sbjct: 116 NYIQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGR 175 Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 A RA ++ ++A L+GV D VIS TF++GA LAA+AG+M YG +GFL G+K+ Sbjct: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKS 235 Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 FTAAV GG+G+L GA++GG+++GLIEA SGY+ GS + D+ F +L+++L Sbjct: 236 FTAAVLGGVGSLPGAMLGGVVIGLIEAFWSGYV--------GSEWKDVATFSILVLVLIF 287 Query: 296 RPSGLLG 302 RP+GLLG Sbjct: 288 RPTGLLG 294 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: 291 Number of extensions: 17 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: 301 Length adjustment: 27 Effective length of query: 282 Effective length of database: 274 Effective search space: 77268 Effective search space used: 77268 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