Align ABC transporter permease (characterized, see rationale)
to candidate WP_028584460.1 G494_RS0110180 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000429965.1:WP_028584460.1 Length = 300 Score = 263 bits (673), Expect = 3e-75 Identities = 140/309 (45%), Positives = 206/309 (66%), Gaps = 11/309 (3%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+ ++ + +GL GS+YALIALGYTMVYGII LINFAHGE+ MIGA T+ + Sbjct: 1 MEYFIELLFSGLTRGSIYALIALGYTMVYGIIGLINFAHGEIYMIGAFTALVVSTAL--T 58 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 + G P +++L + A V AA+ + IE++AYRPLRS+PRL+PLI+AIGMSI LQ + Sbjct: 59 IYGFPLLAVVVLTALAAAVWAASYGYTIERLAYRPLRSAPRLSPLISAIGMSIFLQNYVL 118 Query: 121 IIWKPNYKPYPTMLPSSPF-EIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 + ++ P+P ++P F E + + + IL V+A+A+ L ++ +T G+AMRA Sbjct: 119 LAQTSDFVPFPALVPEFAFMEPYAHIVGSSDMAILVVSALAMIILTCMIKYTRTGKAMRA 178 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 TA++ ++A L+G+ D VIS TFI G+ LAAI G++ AS+ G +GF+ G+KAFTAA Sbjct: 179 TAQDQKMALLVGINVDNVISITFITGSALAAIGGLLIASHIGQINFYIGFIAGIKAFTAA 238 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GGIG++ GAV+G +LGL EA +GY+ S Y D+FAF +L++IL +P+G Sbjct: 239 VLGGIGSIPGAVLGSFILGLTEAFATGYV--------SSDYEDVFAFSLLVLILIFKPAG 290 Query: 300 LLGERVADR 308 LLG+ ++ Sbjct: 291 LLGKATIEK 299 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: 258 Number of extensions: 14 Number of successful extensions: 5 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: 300 Length adjustment: 27 Effective length of query: 282 Effective length of database: 273 Effective search space: 76986 Effective search space used: 76986 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