Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS28270 BPHYT_RS28270 ABC transporter substrate-binding protein
Query= uniprot:D8IUY1 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS28270 Length = 373 Score = 399 bits (1025), Expect = e-116 Identities = 201/366 (54%), Positives = 254/366 (69%), Gaps = 3/366 (0%) Query: 11 IAASLALIPAFAMAQETQVV-KIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGG 69 + A+ + F ++ QVV IG S+PLTGPQA GKDN+ G +AI+ LN +TV G Sbjct: 6 MTAAALMAAGFTLSASAQVVVTIGHSAPLTGPQAPNGKDNENGARLAIDELNKSGVTVAG 65 Query: 70 KKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVATV 129 +K+ F + +EDDQADPK GV VAQKL D GV A+VGPYNSGV IPASRVYN + + V Sbjct: 66 QKVTFKLDSEDDQADPKIGVQVAQKLVDSGVVAVVGPYNSGVAIPASRVYNTGNVPMLPV 125 Query: 130 ASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189 ASNP +T+QGF +FR+ ASD QLGG M +AAK LK K AVIDDRTAYGQG+A++F+K Sbjct: 126 ASNPALTRQGFKNIFRIGASDEQLGGTMGQFAAKTLKAKTAAVIDDRTAYGQGVAEQFVK 185 Query: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDV 249 VAKANGI +V +FTN ATDF +ILT+IK K PD +F GGYA QG P+ +QM+Q G+ Sbjct: 186 VAKANGIQIVEQEFTNSSATDFLSILTTIKAKNPDVIFFGGYAAQGAPMAKQMRQRGLRA 245 Query: 250 PLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAV 309 L+GGDGICS +MG++ G+A VYC QGG L+K G+ F +Y+ YN + YAV Sbjct: 246 KLLGGDGICSADMGKVAGEA-ASIVYCAQGGIALEKTAAGREFLQKYKAAYNIDTQVYAV 304 Query: 310 SFYDGMMLIAQAM-KQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFK 368 S+YDG+ L+A AM K + D + LAK +YKGVAG Y FD DLK +P TVY K Sbjct: 305 SYYDGVKLLADAMVKAGTTTDKAKLTAQLAKENYKGVAGTYSFDEYGDLKGAPTTVYVIK 364 Query: 369 DGLPVP 374 +GLP P Sbjct: 365 NGLPTP 370 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: 488 Number of extensions: 22 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: 378 Length of database: 373 Length adjustment: 30 Effective length of query: 348 Effective length of database: 343 Effective search space: 119364 Effective search space used: 119364 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