Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate GFF1279 Psest_1312 ABC-type branched-chain amino acid transport systems, periplasmic component
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__psRCH2:GFF1279 Length = 372 Score = 296 bits (757), Expect = 8e-85 Identities = 152/354 (42%), Positives = 218/354 (61%), Gaps = 2/354 (0%) Query: 7 LLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 + +A+A T + AD I + AGP+TG A +G+ G E A+ IN AGGV G + Sbjct: 10 IFLAMALTGAASYTLAADTIRIGLAGPVTGPVAQYGDMQFIGAEMAIEQINKAGGVNGAQ 69 Query: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 LK DDACDPKQAVAVAN++ VKFV GH CS S+ PAS +Y +EG+L I+ AST+ Sbjct: 70 LKGVRYDDACDPKQAVAVANKIVNDNVKFVVGHLCSSSTQPASDIYEDEGILMITAASTS 129 Query: 126 PKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALN 185 P +T + + +FR G D QG AG ++ ++ K KNVA++HDK YG+G+A ++ L Sbjct: 130 PDITSRGYELIFRTIGLDSLQGPTAGNFIADHVKPKNVAVIHDKQQYGEGIATAVKQTLE 189 Query: 186 AGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIV 245 K ++E AG+KD+S+L++KLK+E VD VY GGYH E GLL RQ K++GLN + Sbjct: 190 GKNIKVGLFEGINAGDKDFSSLIAKLKREGVDFVYYGGYHPELGLLLRQSKEKGLNVRFM 249 Query: 246 SGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTYAA 304 + + +E AI GPA E +T + P KE V+ F+ +P G + YAA Sbjct: 250 GPEGVGNSEISAIAGPASEGMYVTLPKSFDQDPRNKELVDGFKAKKQDPSGPFVFPAYAA 309 Query: 305 LQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358 +Q+ AE ++A STD+ K+A+ LR N+++T G + FD KGD+ +V Y W+ Sbjct: 310 VQVIAEGIEKAGSTDTDKVAEALRSNTFDTPTGMLSFDEKGDLKDFNFVVYEWH 363 Lambda K H 0.312 0.129 0.366 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: 390 Number of extensions: 18 Number of successful extensions: 2 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: 366 Length of database: 372 Length adjustment: 30 Effective length of query: 336 Effective length of database: 342 Effective search space: 114912 Effective search space used: 114912 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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