Align ABC transporter permease (characterized, see rationale)
to candidate WP_050461646.1 AKL27_RS04820 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_001189915.1:WP_050461646.1 Length = 309 Score = 402 bits (1033), Expect = e-117 Identities = 202/309 (65%), Positives = 251/309 (81%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MDI +QQIINGLVLGSMYALIALGYTMVYG++ LINFAHG+VLMIGA+ S + ++Q Sbjct: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDVLMIGAMAGLSILKLVQHL 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 P PG V L++A + A V ++ +IE+VAYRPLR++PRLAPLITAIG+SILLQTLAM Sbjct: 61 APELPGIVKLIIAIVGAIPVCVIISLIIERVAYRPLRNAPRLAPLITAIGVSILLQTLAM 120 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 +IW + P+P ++PS P I GA I+PTQI++L + A+ +LV +V T +GRAMRAT Sbjct: 121 MIWGRSPVPFPQIMPSDPIHIAGALISPTQIMLLLLALAAMIALVLMVEKTKMGRAMRAT 180 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 AENPR+A LMGV + V+ TF IGA LAAIAG+M+A+NY TAQ MGF+PGLKAF+AAV Sbjct: 181 AENPRIAGLMGVDANRVVVVTFAIGAALAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAV 240 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GGIGN+ GA++GGILLGLIE++G+GYIG LTG LGS+Y DIFAFIVLII+LTLRPSG+ Sbjct: 241 LGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGDFLGSNYQDIFAFIVLIIVLTLRPSGI 300 Query: 301 LGERVADRA 309 +GERVADRA Sbjct: 301 MGERVADRA 309 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: 312 Number of extensions: 5 Number of successful extensions: 1 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: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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