Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate BPHYT_RS12835 BPHYT_RS12835 dihydrolipoamide acetyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >FitnessBrowser__BFirm:BPHYT_RS12835 Length = 550 Score = 224 bits (571), Expect = 5e-63 Identities = 152/444 (34%), Positives = 242/444 (54%), Gaps = 45/444 (10%) Query: 2 GTHVIKMPDIGE--GIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIA 59 G +K+PDIG+ I +E++V KVGD V ++Q L + +DKA +D+PS G V Sbjct: 115 GLQEVKVPDIGDYKDIPVIEVAV---KVGDRVEKEQSLVTLESDKATMDVPSSAAGVVKE 171 Query: 60 LGGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAP 119 + + G+ ++ GSV++ +E EG +A PAP AP A + + + P APA Sbjct: 172 VKVKVGDTVSEGSVIVIVEAEGGA----AAAPAP----APKQAVEKPSDAPATPSPAPAA 223 Query: 120 KAAVCQGPMV------AREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDA 173 +A+ Q P++ AR A ASP+VRK A +LG+ + V+GTGP R+ D+ A Sbjct: 224 PSALAQAPVIPAGEGGARHASH---ASPSVRKFARELGVDVTQVQGTGPKNRITQADVTA 280 Query: 174 YLA---QGQ----SNASAPVAAAYAQRTDEQQIPVIGMRR------KIAQRMQDATQRAA 220 ++ GQ + A+AP AA + P + + K R++ + Sbjct: 281 FIKGVMTGQRAAPAGAAAPAAAGGGGELNLLPWPKVDFTKFGPVDPKPLSRIKKISGANL 340 Query: 221 HFSYV--------EEIDVTAVEELRAHLNEKHGATRGKLTLLPFLVRALVVALRDFPQIN 272 H ++V +E D+T +E LR LN+++ + K+T+L F+++A+V AL+ FP N Sbjct: 341 HRNWVMIPHVTNNDEADITELEALRVKLNKEYEKSGVKITMLAFVIKAVVSALKQFPTFN 400 Query: 273 ARYDDEAQVITRLGAVHVGIATQADIGLMVPVVRHAEARSLWDSAAEISRLATAARNGKA 332 A D + V + H+G A GL+VPV+R A+ + L D A E++ L+ AR+GK Sbjct: 401 ASLDGDNLVFKQY--FHIGFAADTPNGLVVPVIRDADKKGLIDIAKEMAELSKLARDGKL 458 Query: 333 SRDELSGSTITLTSLGALGGIVSTPVLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLS 392 D++ G +++SLG +GG TP++N PEVAI+G+++ +P+ Q V R + LS Sbjct: 459 KPDQMQGGCFSISSLGGIGGTNFTPIINAPEVAILGLSRGAMKPVWDGKQFVPRLTLPLS 518 Query: 393 SSFDHRVVDGMDAALFIQAIRGLL 416 S+DHRV+DG AA F + LL Sbjct: 519 LSYDHRVIDGAAAARFNAYLGALL 542 Score = 58.2 bits (139), Expect = 6e-13 Identities = 39/117 (33%), Positives = 63/117 (53%), Gaps = 11/117 (9%) Query: 6 IKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIALGGQPG 65 +K+PDIG+ ++ + VK GD V ++Q L + +DKA +D+PS G V + + G Sbjct: 7 VKVPDIGD-YKDIPVIEVLVKAGDTVEKEQSLVTLESDKATMDVPSSAAGVVKEVKVKVG 65 Query: 66 EVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPKAA 122 + ++ GS+++ + EGA + PAP AP AA + P AAP P A+ Sbjct: 66 DNVSEGSLIVVL--EGAEGGAAAPAPAPAAAPAPSAA--------AAPAAAPVPAAS 112 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: 514 Number of extensions: 25 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 425 Length of database: 550 Length adjustment: 34 Effective length of query: 391 Effective length of database: 516 Effective search space: 201756 Effective search space used: 201756 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: 52 (24.6 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