Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate BWI76_RS04885 BWI76_RS04885 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Koxy:BWI76_RS04885 Length = 629 Score = 228 bits (582), Expect = 3e-64 Identities = 145/432 (33%), Positives = 221/432 (51%), Gaps = 39/432 (9%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G E E+ E VK GD + + L V DKA++E+P+P G V + G Sbjct: 208 VHVPDIGGD--EVEVTEVMVKVGDKIAAEQSLITVEGDKASMEVPAPFAGTVKEIKISTG 265 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V+ + ++ E G A AAP A ++ A AP Q KPA P Sbjct: 266 DKVSTGSLIMVFEVEGAAPAAAP----------------AAAAPAPAAAPAQAAKPAAAP 309 Query: 126 APAPR---EAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISRG-- 180 A E + A A+P +R ARE G++L +V G+G GRI ED+ ++ Sbjct: 310 AAKAEGKSEFAENDAYVHATPLIRRLAREFGVNLAKVKGSGRKGRILREDVQAYVKEAVK 369 Query: 181 -AEPLPAQTG-------------LVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226 AE PA TG + VEEV + +++ +S + IPH+T+ + Sbjct: 370 RAEAAPAATGGGIPGMLPWPKVDFSKFGEVEEVELGRIQKISGANLSRNWVMIPHVTHFD 429 Query: 227 EVDMTALEDLRATMNRDRKPEQ--AKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHR 284 + D+T LE R N + + + K T + F+M+A+ + + P N++ + A + Sbjct: 430 KTDITDLEAFRKQQNAEAEKRKLDVKFTPVVFIMKAVAAALEQMPRFNSSLSEDAQRLTL 489 Query: 285 HAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITI 344 ++IG+A TP GL VPV + + I + + EL ++ AR G T E+ G TI Sbjct: 490 KKYINIGVAVDTPNGLVVPVFKDVNKKSITELSRELTVISKKARDGKLTAGEMQGGCFTI 549 Query: 345 SSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWD 404 SS+G +G P++N PEVAI+GV+K A+ PVW+G +FVPR +M +S SFDHRVIDG D Sbjct: 550 SSIGGLGTTHFAPIVNAPEVAILGVSKSAMEPVWNGKEFVPRLMMPISLSFDHRVIDGAD 609 Query: 405 AAVFVQRLKTLL 416 A F+ + +L Sbjct: 610 GARFITIINNML 621 Score = 55.8 bits (133), Expect = 4e-12 Identities = 36/104 (34%), Positives = 51/104 (49%), Gaps = 2/104 (1%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G E E+ E VK GD V + L V DKA++E+PSP G V + VG Sbjct: 5 IKVPDIGAD--EVEITEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGVVKEIKVSVG 62 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSR 109 D ++ ++A A AAP + A P A S++ Sbjct: 63 DKTETGKLIMIFDSADGAAAAAPAQEEKKEAAPAAAAPAAASAK 106 Lambda K H 0.317 0.133 0.384 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: 636 Number of extensions: 19 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 426 Length of database: 629 Length adjustment: 35 Effective length of query: 391 Effective length of database: 594 Effective search space: 232254 Effective search space used: 232254 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: 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