Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate 8501892 DvMF_2607 Extracellular ligand-binding receptor (RefSeq)
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Miya:8501892 Length = 372 Score = 214 bits (546), Expect = 2e-60 Identities = 121/364 (33%), Positives = 189/364 (51%), Gaps = 4/364 (1%) Query: 7 LLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 L+ +A M AD I AG +G A++G + INA GGVLG++ Sbjct: 9 LVAGLAVAVMACPAFAADTIKFGVAGAHSGDLASYGLPTVNAAKLVAKMINAKGGVLGKQ 68 Query: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 +++ DD C P+ A A +L G V GH CSG++ A +Y E ++ +SP++TN Sbjct: 69 VEVIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEANIVLMSPSATN 128 Query: 126 PKLTEQ-NLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184 P LT+ + N FR DDQQ ++ + ++ K +A+LHDK YGKG A+ ++ + Sbjct: 129 PALTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGKGYAEYAKQFV 188 Query: 185 NAGGQKEKI-YEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAP 243 G+ + +E T G DYSA+V K++ + V GGYH EA + +Q++ + ++ P Sbjct: 189 EQSGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQQLRKKRMDLP 248 Query: 244 IVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVE-KFRKAGYEPEGYTLYTY 302 VS D + + + + G E + D +P KEA+E ++ G EP + Y Sbjct: 249 FVSDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGAEPGAFYKEAY 308 Query: 303 AALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQY 362 AA A ++A STDSAKI + LR T +GKI FD +GD + Y+ NG+Y Sbjct: 309 AASLALLNAIEKAGSTDSAKIMNALRTEFVETSVGKIKFDKRGDAEGVGFSMYQVKNGKY 368 Query: 363 AQVK 366 ++K Sbjct: 369 VELK 372 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: 376 Number of extensions: 20 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: 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