Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate AO353_12860 AO353_12860 dihydrolipoamide acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12860 Length = 544 Score = 255 bits (651), Expect = 3e-72 Identities = 159/428 (37%), Positives = 228/428 (53%), Gaps = 28/428 (6%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 120 IHVPDIGSS-GKAKIIEVLVKVGDTVEADQSLITLESDKASMEIPSPAAGVVESIAVKLE 178 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V +++++ AG A AAP P A A P A ++ AK + PAP Sbjct: 179 DEVGTGDFILKLKVAGAAAPAAP--APAAAAPAQAAAPAAAAAAPVAKT--EAAAPAPVS 234 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179 APAP AK A PAVR ARE G++L V+ +GP GR+ ED+ +++ Sbjct: 235 APAPS-----GAKVHAGPAVRQLAREFGVELNAVSPSGPHGRVLKEDVQVYVKAMMQKAK 289 Query: 180 -----------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEV 228 G P+P R +EEV M L + A + S +PH+T + Sbjct: 290 EAPAAGATGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQAGAANLHRSWLNVPHVTQFDSA 348 Query: 229 DMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAV 288 D+T LE R + KLT+LP L+++ + E P N++ I R V Sbjct: 349 DITELEAFRVAQKAVAEKAGVKLTVLPLLLKSCAHLLKELPDFNSSLAPSGKAIIRKKYV 408 Query: 289 HIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLG 348 +IG A TP GL VPV+++ + + + AAE LA+ ART + DE+ G+ TISSLG Sbjct: 409 NIGFAVDTPEGLLVPVIKNVDQKSLLQLAAEAASLAEKARTKKLSADEMQGACFTISSLG 468 Query: 349 AIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVF 408 IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G AA F Sbjct: 469 HIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAARF 528 Query: 409 VQRLKTLL 416 +RL LL Sbjct: 529 TKRLSDLL 536 Score = 68.9 bits (167), Expect = 4e-16 Identities = 46/139 (33%), Positives = 67/139 (48%), Gaps = 16/139 (11%) Query: 5 IIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEV 64 +I++PD+G G E E++E VK GD + D L + +DKA++EIP+P G + L ++ Sbjct: 4 LIRVPDIGSG--EGEVIELLVKVGDRIEADQSLLTLESDKASMEIPAPKAGVIKSLKVKL 61 Query: 65 GDTVAVKAPLVRIETAG-EAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAP 123 GD + L+ +E G A AAP + P A A A AP PAP Sbjct: 62 GDRLKEGDELMELEVEGAAAAPAAPAAAPAAAA-------------APAAAPAPQAAPAP 108 Query: 124 KPAPAPREAPDLSAKPLAS 142 APA D+ + S Sbjct: 109 AAAPAAATVQDIHVPDIGS 127 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: 569 Number of extensions: 22 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: 426 Length of database: 544 Length adjustment: 34 Effective length of query: 392 Effective length of database: 510 Effective search space: 199920 Effective search space used: 199920 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: 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