Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate H281DRAFT_00467 H281DRAFT_00467 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_00467 Length = 562 Score = 232 bits (591), Expect = 2e-65 Identities = 157/440 (35%), Positives = 243/440 (55%), Gaps = 35/440 (7%) Query: 2 GTHVIKMPDIGE--GIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIA 59 G +K+PDIG+ I +E++V KVGD V ++Q L + +DKA +D+PS G V Sbjct: 125 GLQDVKVPDIGDYKDIPVIEVAV---KVGDRVEKEQSLVTLESDKATMDVPSSAAGVVKE 181 Query: 60 LGGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAP 119 + + G+ ++ GSV++ +E EGA +A PAP AP T+ + P APA Sbjct: 182 VKVKVGDTVSEGSVIVVVEAEGA-----AAAPAPAPAAAPKQQTEKPSDAPVTPSPAPAS 236 Query: 120 KAAVCQGPMV-AREADER--PLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLA 176 +A+ Q P++ A E R ASP+VRK A +LG+ + V+GTGP GR+ D+ A++ Sbjct: 237 PSALAQAPVIPAGEGGARHPSHASPSVRKFARELGVDVTQVQGTGPKGRITQADVTAFIK 296 Query: 177 ---QGQSNASAPVAAAYAQRTDEQQI---PVIGMRR------KIAQRMQDATQRAAHFSY 224 GQ A A AA A E + P I + K R++ + H ++ Sbjct: 297 GVMTGQRAAPAGAAAPAAAGGGELNLLPWPKIDFTKFGPVDPKPLSRIKKISGANLHRNW 356 Query: 225 V--------EEIDVTAVEELRAHLNEKHGATRGKLTLLPFLVRALVVALRDFPQINARYD 276 V +E D+T +E LR LN+++ K+T+L F+++A+V AL+ FP NA D Sbjct: 357 VMIPHVTNNDEADITELEALRVQLNKENEKAGVKITMLAFVIKAVVSALKKFPTFNASLD 416 Query: 277 DEAQVITRLGAVHVGIATQADIGLMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDE 336 + V + HVG A GL+VPV+R A+ + L + A E++ L+ AAR GK D+ Sbjct: 417 GDNLVFKQY--YHVGFAADTPNGLVVPVIRDADKKGLVEIAKEMTDLSKAAREGKLKPDQ 474 Query: 337 LSGSTITLTSLGALGGIVSTPVLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFD 396 + G +++SLG +GG TP++N PEVAI+G+++ +P+ Q V + M+ LS S+D Sbjct: 475 MQGGCFSISSLGGIGGTNFTPIINAPEVAILGLSRGAMKPVWDGKQFVPKLMLPLSLSYD 534 Query: 397 HRVVDGMDAALFIQAIRGLL 416 HRV+DG +AA F + LL Sbjct: 535 HRVIDGAEAARFNAYLGALL 554 Score = 65.9 bits (159), Expect = 3e-15 Identities = 40/117 (34%), Positives = 64/117 (54%), Gaps = 5/117 (4%) 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+++ ++ G G +A PAP AP AA + P APAP AA Sbjct: 66 DNVSEGSLIVVLDGAGGG----AAAPAPAAAPAPAAAPAPAAAPAAAPAPAPAPAAA 118 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: 557 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 425 Length of database: 562 Length adjustment: 34 Effective length of query: 391 Effective length of database: 528 Effective search space: 206448 Effective search space used: 206448 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