Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate GFF3112 HP15_3055 high-affinity leucine-specific leucine-specific-binding periplasmic protein of high-affinity branched-chain amino acid ABC transporter transport system periplasmic binding protein
Query= uniprot:D8IUY1 (378 letters) >FitnessBrowser__Marino:GFF3112 Length = 370 Score = 176 bits (446), Expect = 9e-49 Identities = 113/367 (30%), Positives = 187/367 (50%), Gaps = 11/367 (2%) Query: 11 IAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGK 70 ++ S+AL+ A A E Q IG + P+TGP A G G MAIE++NA +G + Sbjct: 12 VSTSVALMGAGHAAAEIQ---IGIAGPMTGPVAQYGDMQFSGARMAIEQINANGGVMGEE 68 Query: 71 KIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVATVA 130 + + DD DPK V VA L + GV+ ++G S T PAS +Y D GI++ T A Sbjct: 69 LV---AVEYDDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGILMVTPA 125 Query: 131 S-NPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189 S +P+IT++G+ +FR DS G A Y A + +RVA++ D+ YG+G+A Sbjct: 126 STSPEITERGYELVFRTIGLDSMQGPVAARYIASQNP-ERVAIVHDKQQYGEGIATAVRD 184 Query: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDV 249 K G+++ + DF++++T +K D V+ GGY P+ G I RQ +D Sbjct: 185 TLKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANSADLDA 244 Query: 250 PLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAV 309 MG +G+ + ++ + G+A E + T D+ E + ++ K P+ + + Sbjct: 245 RFMGPEGVGNKDINTIAGEA-AEGLLVTL-PPAFDQKAENQALVKAFEDKGEDPSGPFVL 302 Query: 310 SFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRF-K 368 + Y + L+A+ ++ A S DP AL + +++ G ++D D+K VY + Sbjct: 303 TSYTAVQLVAEGIEAAGSTDPFDVAAALREGTFQTPIGTVEYDKAGDMKSFEFVVYEWHS 362 Query: 369 DGLPVPL 375 DG P+ Sbjct: 363 DGSKTPV 369 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: 396 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 378 Length of database: 370 Length adjustment: 30 Effective length of query: 348 Effective length of database: 340 Effective search space: 118320 Effective search space used: 118320 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: 50 (23.9 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