Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_015948683.1 G491_RS0116410 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_000429905.1:WP_015948683.1 Length = 372 Score = 198 bits (504), Expect = 2e-55 Identities = 124/359 (34%), Positives = 194/359 (54%), Gaps = 8/359 (2%) Query: 5 LSLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQ 64 L L+ A++ A ++A + + PITG +A G+ MK+ E +NA GG+LG+ Sbjct: 5 LFLIAALSIIAAGTALAADTVKIGLTAPITGSWAAEGQDMKQICELLADQVNADGGLLGK 64 Query: 65 KLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPAST 124 ++++ V DD + + A A +LA G+ V G + S + + +Y + QI+ ST Sbjct: 65 EVEVVVADDGGNEQTAALAAQRLATKGIVAVVGTYGSSVTEASQGIYNAAKIPQIANGST 124 Query: 125 NPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184 +LTE+ LK FR RDD+QG++A K L+ K +AILHD + Y KGLA+ET+ L Sbjct: 125 AVRLTEKGLKYFFRTSPRDDEQGRVAAKTLM-GMGYKKIAILHDNTTYAKGLAEETKALL 183 Query: 185 NAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPI 244 + + ++A T GE+DY+ +++ LK + +VV+ GY+ EAGL+ RQ K+ G + P Sbjct: 184 DKEPVELVFFDALTPGEQDYTTILTTLKTKNAEVVFFTGYYPEAGLMLRQKKEMGFDVPF 243 Query: 245 VSGDALVTNEYWAITG-PAGENTMMTFGPDPREMP--EAKEAVEKF-RKAGYEPEG-YTL 299 V GDA + I G A E P P+++P EAK+ + + +K G P + + Sbjct: 244 VGGDATNNPDLVKIAGKDAAEGFYFISPPVPQDLPSKEAKDFLAAYTKKYGAAPGSIWAV 303 Query: 300 YTYAALQIWAEAAKQANSTDSAKIADVLR--KNSYNTVIGKIGFDAKGDVTSPAYVWYR 356 + ++ EA KQ NSTD KIAD L + + G I F+ KGD Y Y+ Sbjct: 304 LSGDGFRVMVEAIKQTNSTDPNKIADYLHTGMKDFPGLTGTISFNEKGDRVGDVYRVYK 362 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: 356 Number of extensions: 23 Number of successful extensions: 3 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 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