Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_012275606.1 SHAL_RS02430 dihydrolipoyllysine-residue acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_000019185.1:WP_012275606.1 Length = 555 Score = 237 bits (605), Expect = 6e-67 Identities = 154/432 (35%), Positives = 228/432 (52%), Gaps = 30/432 (6%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G+ ++ +++E V GD + D L + TDKAT+E+P+P G V L VG Sbjct: 125 VSVPDIGDA-SDVDVIEVLVAVGDKIDADTGLITLETDKATMEVPAPSAGIVKELKVAVG 183 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V++ + ++ +E + +A AAP A + P V+ A PP P P+ Sbjct: 184 DKVSMGSLVLMLEVS-DAAPAAPVVAAPATSTPAPVAPAPVAQAASANKPPVPHHPSAGS 242 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFI-------- 177 P + ASPAVR ARE G DL V GTG GRI ED+ FI Sbjct: 243 QPK-------TGAVHASPAVRRLAREFGADLTLVKGTGRKGRILKEDVQAFIKYELSRPK 295 Query: 178 -------SRGAEPLPA----QTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226 + GA L + + VEEV + +++ + + IPH+T + Sbjct: 296 ASAATAVAGGAGGLSVIAAPKVDFAKFGEVEEVPLSRIQKISGPNLHRNWVTIPHVTQFD 355 Query: 227 EVDMTALEDLRATMNR--DRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHR 284 E D+T LE R N +K K+T L F+M+A+ KT+AE P N++ + + Sbjct: 356 EADITELEAFRKDQNAVAAKKKADYKITPLVFMMKAVAKTLAEFPVFNSSLSADGESLIQ 415 Query: 285 HAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITI 344 HIG+A TP GL VPVVR + +GI + + EL ++ AR G ++ GS TI Sbjct: 416 KKYFHIGVAVDTPNGLMVPVVRDVDKKGIVELSRELTEISVKARDGKLKAADMQGSCFTI 475 Query: 345 SSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWD 404 SSLG IGG A TP++N+P+VAI+GV+K ++P W+G +F P+ ++ LS S+DHRVIDG Sbjct: 476 SSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRVIDGAM 535 Query: 405 AAVFVQRLKTLL 416 AA F L ++L Sbjct: 536 AARFSVTLSSIL 547 Score = 54.7 bits (130), Expect = 7e-12 Identities = 37/121 (30%), Positives = 58/121 (47%), Gaps = 10/121 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G E +++E GD + + + V +DKAT++IP+P G + L VG Sbjct: 7 VLIPDIGGD--EVQVIEICAAVGDTLAAEESIITVESDKATMDIPAPFAGVLSELKVAVG 64 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 DTV+ + + AG +S P A P AV + + A+AP E PA Sbjct: 65 DTVSEGTLIAMMSAAGAQAPTEVESTPAA--------PDAVQAPVAAQAPAPEEAPAASV 116 Query: 126 A 126 A Sbjct: 117 A 117 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: 547 Number of extensions: 28 Number of successful extensions: 5 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: 426 Length of database: 555 Length adjustment: 34 Effective length of query: 392 Effective length of database: 521 Effective search space: 204232 Effective search space used: 204232 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 24 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