Align ABC transporter permease (characterized, see rationale)
to candidate WP_013519967.1 ALIDE2_RS06405 high-affinity branched-chain amino acid ABC transporter permease LivH
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000204645.1:WP_013519967.1 Length = 308 Score = 253 bits (647), Expect = 3e-72 Identities = 141/307 (45%), Positives = 197/307 (64%), Gaps = 19/307 (6%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 LLQQ+ NGL LG++YALIA+GYTMVYGII +INFAHGE+ MIGA + + G G Sbjct: 8 LLQQLFNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYAGLVTLAAI-GTQSG 66 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 P VI+ L ++A +V FV+E+VAY+PLR+ PRL LI+AIGMSI LQ + Sbjct: 67 LPVAVIIALMLLVAVLVTGVYGFVVEQVAYKPLRNGPRLVALISAIGMSIFLQNWVALGQ 126 Query: 124 KPNYKPYPTMLPS-------SPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRA 176 P++LP S FE+ F+ T++LI+ VT V + +L + H+ +GRA Sbjct: 127 GARDMAVPSLLPGALRFGDESGFEV---FVPYTRVLIIVVTVVLMIALTLYIRHSRMGRA 183 Query: 177 MRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAF 236 RA +++ +A L+G+ + VIS TFI+GAVLAA+ G++ A G +GF+ G+KAF Sbjct: 184 SRACSQDMHMAGLLGIDVNRVISFTFILGAVLAAVGGVLIALAVGKLNPFIGFIVGVKAF 243 Query: 237 TAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLR 296 TAAV GGIG++ GA++GG+LLG+ E + YI S Y DI AF +L++IL R Sbjct: 244 TAAVLGGIGSIPGAMLGGVLLGVAETFAAAYI--------SSEYKDIVAFGLLVLILLFR 295 Query: 297 PSGLLGE 303 P+GLLG+ Sbjct: 296 PTGLLGK 302 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: 286 Number of extensions: 15 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: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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