Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_090272111.1 BLU11_RS03770 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_900105005.1:WP_090272111.1 Length = 375 Score = 291 bits (746), Expect = 1e-83 Identities = 150/357 (42%), Positives = 220/357 (61%), Gaps = 3/357 (0%) Query: 5 LSLLVAVAATAMTASVAKA--DIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVL 62 LS VAV A A +S+ A I +A AGP+TG A +G+ G A+ IN AGGV Sbjct: 9 LSQFVAVTALAGISSLTLAAETIRIALAGPVTGAVAQYGDMQFTGANMAIDMINKAGGVN 68 Query: 63 GQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPA 122 G +L+ V DDACDPKQAVAVAN++ G+ FV GH CS S+ PA+ +Y +EG+L ++PA Sbjct: 69 GSQLEGVVFDDACDPKQAVAVANRIVNDGISFVVGHLCSSSTQPATDIYEDEGILMVTPA 128 Query: 123 STNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQK 182 +T+P +T + + +FR G D QG AGK+++EN K + VA++HDK YG+G+A + Sbjct: 129 ATSPDITSRGYELIFRTIGLDSLQGPTAGKFIVENIKPEKVAVIHDKQQYGEGIATAVRG 188 Query: 183 ALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242 L G I++ TAG+KD+SAL+++L+Q VD VY GGYH E GL+ RQ ++QGLN Sbjct: 189 VLTEAGIDVPIFDGITAGDKDFSALIARLRQAQVDFVYFGGYHPELGLILRQAREQGLNV 248 Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYT 301 + + + ++ AI G A E ++T E P VE F++ +P G + + Sbjct: 249 KFMGPEGVGNSDISAIAGAAAEGMLVTLPKAFDEDPANAPLVEAFKERKQDPRGPFVFPS 308 Query: 302 YAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358 YAA+Q+ A+ + A STD +A+ LR N+++T GK+ FD KGD+ +V Y W+ Sbjct: 309 YAAVQVIADGIRLAESTDPFDVAEALRNNTFDTPTGKLAFDEKGDLKDFNFVVYEWH 365 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: 383 Number of extensions: 16 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: 375 Length adjustment: 30 Effective length of query: 336 Effective length of database: 345 Effective search space: 115920 Effective search space used: 115920 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 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