Align ABC transporter permease (characterized, see rationale)
to candidate WP_011767542.1 AZO_RS19170 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000061505.1:WP_011767542.1 Length = 285 Score = 139 bits (351), Expect = 6e-38 Identities = 90/302 (29%), Positives = 149/302 (49%), Gaps = 20/302 (6%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M Q + +G+ G +Y L+AL + ++Y ++F GE+LM+GA ++ +G+ Sbjct: 1 MSAFAQVLASGVATGCVYGLVALSFVLIYKASDTVSFMQGELLMVGA---FAAVGLHAAG 57 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 +P L LA ++A + A L +E++A R P L ++ G ++++ Sbjct: 58 VP-------LALAGVLAVLAVALLGAALERLALRRALGQPHLVAVLLTFGFGLVMRGAVA 110 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 + ++ + LP +GG + + ++ TA+ + L HT G A+RA Sbjct: 111 SVPAATHEMHRLPLPEQVLVLGGIVFASSHLAVIAATALLVLLLALFFRHTRAGLALRAC 170 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 AE+ RVA+LMGV + + + +GA LAA AG++ A MG L LKAF AAV Sbjct: 171 AEDARVAALMGVPVARMHTLAWALGAGLAAFAGLLLAP-ISFVHLDMG-LVALKAFPAAV 228 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GG+ +L GA+ GG+ +G+ EA L G L Y D + +L++ L P G Sbjct: 229 LGGLYSLPGALAGGVFIGVAEA--------LAGLALPEGYKDAVPYALLMLALLAFPRGF 280 Query: 301 LG 302 G Sbjct: 281 GG 282 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: 191 Number of extensions: 9 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: 309 Length of database: 285 Length adjustment: 26 Effective length of query: 283 Effective length of database: 259 Effective search space: 73297 Effective search space used: 73297 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