Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate PP_4403 PP_4403 Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >FitnessBrowser__Putida:PP_4403 Length = 423 Score = 602 bits (1553), Expect = e-177 Identities = 318/425 (74%), Positives = 355/425 (83%), Gaps = 2/425 (0%) Query: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60 MGTHVIKMPDIGEGIA+VEL W VKVGD++ EDQV+ADVMTDKA V+IPSPV GKV+AL Sbjct: 1 MGTHVIKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLAL 60 Query: 61 GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPK 120 GGQPGEVMAVGS LI IEVEG+GN + QP PV A A K E + KP AP Sbjct: 61 GGQPGEVMAVGSELIRIEVEGSGNHVDVPQPKPVEAPAAPIAAKPEPQKDVKPAVYQAP- 119 Query: 121 AAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQS 180 A P+V R+ ++PLASPAVRK ALD GI+LR V G+GPAGR+LHEDLDA++++ QS Sbjct: 120 ANHEAAPIVPRQPGDKPLASPAVRKRALDAGIELRYVHGSGPAGRILHEDLDAFMSKPQS 179 Query: 181 NASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAHL 240 NA YA+RTD +Q+PVIG+RRKIAQRMQDA +R AHFSYVEEIDVTA+E LR L Sbjct: 180 NAGQ-APDGYAKRTDSEQVPVIGLRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALRQQL 238 Query: 241 NEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIGL 300 N KHG +RGKLTLLPFLVRALVVALRDFPQINA YDDEAQ+ITR GAVHVGIATQ D GL Sbjct: 239 NSKHGDSRGKLTLLPFLVRALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQGDNGL 298 Query: 301 MVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVLN 360 MVPV+RHAEA SLW +A EISRLA AARN KASR+ELSGSTITLTSLGALGGIVSTPV+N Sbjct: 299 MVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSGSTITLTSLGALGGIVSTPVVN 358 Query: 361 LPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQPA 420 PEVAIVGVN++VERP+VI GQIV+RKMMNLSSSFDHRVVDGMDAALFIQA+RGLLEQPA Sbjct: 359 TPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGLLEQPA 418 Query: 421 TLFVE 425 LFVE Sbjct: 419 CLFVE 423 Lambda K H 0.318 0.133 0.368 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: 574 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: 425 Length of database: 423 Length adjustment: 32 Effective length of query: 393 Effective length of database: 391 Effective search space: 153663 Effective search space used: 153663 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 (21.7 bits) S2: 51 (24.3 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