Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate WP_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:D8IUY1 (378 letters) >NCBI__GCF_001305595.1:WP_045585058.1 Length = 366 Score = 197 bits (500), Expect = 5e-55 Identities = 123/361 (34%), Positives = 197/361 (54%), Gaps = 8/361 (2%) Query: 11 IAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGK 70 + A++A A A + + + + P+TG A+ G+ + G+ A+ +NA V G+ Sbjct: 7 LLAAIAATALSATAAKADIA-VATAGPITGQYATFGEQMKKGMEQAVADINAAG-GVLGQ 64 Query: 71 KIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIV-VATV 129 K+K +V DD DPK VAVA +LA GVK + G + SG +IPAS+VY + G++ ++ Sbjct: 65 KLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISPA 122 Query: 130 ASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189 ++NPK+T+QG +FRV D Q G Y ++ K K VA++ D++AYG+GLA E K Sbjct: 123 STNPKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQK 182 Query: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDV 249 A G + D++A+++ +K DAV++GGY + G + RQMK G+ Sbjct: 183 ALNAGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLKA 242 Query: 250 PLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAV 309 P++ GD + + E + GDA GE T G +KA + K ++++K P E Y + Sbjct: 243 PIVSGDALVTNEYWAITGDA-GEDTMMTFGPDPREKA-DAKAVVEKFRKAGYEP-EGYTL 299 Query: 310 SFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFKD 369 Y + + A+A+KQA S D + L K SY+ V G+ FDA D+ Y++ + Sbjct: 300 YTYAALQIWAEAVKQAKSTDAAKVSEVLRKGSYETVIGKIGFDAKGDVTSPAYVWYKWHN 359 Query: 370 G 370 G Sbjct: 360 G 360 Lambda K H 0.316 0.134 0.378 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: 405 Number of extensions: 27 Number of successful extensions: 8 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: 378 Length of database: 366 Length adjustment: 30 Effective length of query: 348 Effective length of database: 336 Effective search space: 116928 Effective search space used: 116928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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