Align ABC transporter permease (characterized, see rationale)
to candidate 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein
Query= uniprot:A0A165KC95 (309 letters) >MicrobesOnline__882:206138 Length = 301 Score = 251 bits (642), Expect = 1e-71 Identities = 135/309 (43%), Positives = 196/309 (63%), Gaps = 10/309 (3%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+ LQQ+ NGL +G +YALIALGYTMVYG+++LINFAHG++ IGA ++ + G Sbjct: 1 MEEFLQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAAL-GL 59 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G V +LL T + + A + +++E+VAYRPLRSS RL+ +++A+G SI Q M Sbjct: 60 SGHVSGAVAVLLVTTMVMGLVALIGYLLERVAYRPLRSSSRLSAVVSALGASIFFQNAVM 119 Query: 121 IIWKPNYKPYPTML-PSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 +I+ ++ YP + P+ G I +I++ G + + L + ++ T G A+RA Sbjct: 120 LIYGAKFQVYPNDIRPTMAVSFFGMDIPLVRIMMFGASVALMLLLHFFIHRTRTGTAIRA 179 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 A + A LMG+ + VI+ F+IG L AG+M YG TMG++ GLKAFTAA Sbjct: 180 VAIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTAA 239 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 + GGIGN+ GA+VGG+LLG+IEA+G+ YI + D AF+VLI+IL +RP+G Sbjct: 240 ILGGIGNIPGAMVGGLLLGVIEALGAAYISIA--------WKDAIAFLVLILILIIRPTG 291 Query: 300 LLGERVADR 308 LLGERVAD+ Sbjct: 292 LLGERVADK 300 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: 261 Number of extensions: 13 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 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