Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate BPHYT_RS19350 BPHYT_RS19350 amino acid ABC transporter substrate-binding protein
Query= uniprot:D8IUY1 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS19350 Length = 382 Score = 320 bits (819), Expect = 5e-92 Identities = 166/370 (44%), Positives = 241/370 (65%), Gaps = 6/370 (1%) Query: 3 KRVSGLNIIAA-SLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLN 61 K+++G ++AA SLA A AQ T+ VK+GF+ P+TG QA GKD Q G+ +A+E +N Sbjct: 6 KQLAGAALVAAMSLA---GTANAQSTEDVKVGFAGPMTGAQAHYGKDFQNGITLAVEDMN 62 Query: 62 AQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYND 121 A +GGK+++F + + DDQADP++G VAQKL D G+K ++G +NSG TIPASR+Y + Sbjct: 63 ATKPVIGGKQVRFVLDSADDQADPRTGTTVAQKLVDDGIKGMLGHFNSGTTIPASRIYAN 122 Query: 122 AGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQ 181 AGI +A+ P+ TQQGF T FR+ SD+Q G +A K L K++A++DDRTAYGQ Sbjct: 123 AGIPEIAMATAPEYTQQGFKTTFRMMTSDTQQGSVAGTFAVKTLGVKKIAIVDDRTAYGQ 182 Query: 182 GLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQ 241 GLA +F K AKA G +V ++TNDKA DF +ILT +K +PD ++ GG Q P+ +Q Sbjct: 183 GLADQFEKAAKAAGGQIVDREYTNDKAVDFKSILTKLKSVQPDLIYYGGADSQAAPMVKQ 242 Query: 242 MKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYN 301 MK LG+ PLMGG+ + +P ++ GDA +V + G L++ GK + +Y+K++N Sbjct: 243 MKALGIKAPLMGGEMVHTPTFIQIAGDAANGTV-ASLAGLPLEEMPGGKDYVAKYKKRFN 301 Query: 302 RPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGV-AGQYDFDANHDLKQS 360 +TY+ YDG M + AMK+ANS DP ++ P LAK S V + +D+ DLK Sbjct: 302 EDVQTYSPYAYDGAMAMFDAMKKANSTDPAKYLPVLAKTSMPAVTSANLAYDSKGDLKNG 361 Query: 361 PVTVYRFKDG 370 +T+Y+ DG Sbjct: 362 GITLYKVVDG 371 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: 465 Number of extensions: 20 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: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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