Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= uniprot:D8IUY1 (378 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 160 bits (405), Expect = 5e-44 Identities = 114/360 (31%), Positives = 178/360 (49%), Gaps = 18/360 (5%) Query: 5 VSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQP 64 V L + A+ L+ A A A VKIG PLTG AS G+D + + + + LN Sbjct: 5 VKALTLALAASLLMAATAFAAP---VKIGLMCPLTGKWASEGQDMRNIVTLLADELNKAG 61 Query: 65 ITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGI 124 + G K+ +++ EDD DP++ AQKL GV A +G Y S VT + +Y++AG+ Sbjct: 62 -GINGNKV--ELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGV 118 Query: 125 V-VATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELK---FKRVAVIDDRTAYG 180 V +AT ++ ++T++G R A D + G + AAK +K +K VA++ D ++Y Sbjct: 119 VQIATGSTAVRLTEKGLKRFLRTAPRDDEQG----MVAAKLIKAKGYKAVALLHDNSSYA 174 Query: 181 QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR 240 +GLA E + G +V D D+TAILT +K PD +F GY P+ G + R Sbjct: 175 KGLADETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLR 234 Query: 241 QMKQLGVDVPLMGGDGICSPEMGRLGG-DAIGESVYCTQGGTMLDKAKEGKVFSDEYQKK 299 Q ++ +VP+MGGD ++ ++ G +A + + G A K Y+ K Sbjct: 235 QKMEMKWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAK 294 Query: 300 YNR-PAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPAL-AKI-SYKGVAGQYDFDANHD 356 YN P ++V D +I +A+K D L K+ +Y G GQ F+ D Sbjct: 295 YNGVPGSVWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGD 354 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: 359 Number of extensions: 14 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: 375 Length adjustment: 30 Effective length of query: 348 Effective length of database: 345 Effective search space: 120060 Effective search space used: 120060 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