Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate PP_0338 PP_0338 AceF-S-acetyldihydrolipoate
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Putida:PP_0338 Length = 546 Score = 251 bits (640), Expect = 5e-71 Identities = 162/434 (37%), Positives = 228/434 (52%), Gaps = 38/434 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 120 IHVPDIGSS-GKAKIIEVLVKVGDTVEADQSLITLESDKASMEIPSPAAGVVEEVLCKLE 178 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQ--PEKPAP 123 D V + +++ AG A AAP P A + +A+A P P AP Sbjct: 179 DEVGTGDLIFKLKVAGAAPAAAP-------------APAAAPAPAKAEAAPAAAPAAAAP 225 Query: 124 KPAPAPRE---APDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR- 179 APAP A +AK A PAVR ARE G++L VA TGP GRI ED+ +++ Sbjct: 226 AAAPAPAATAPAAGSNAKVHAGPAVRQLAREFGVELGAVAATGPHGRILKEDVQVYVKAM 285 Query: 180 -----------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHI 222 G P+PA + VEEV + L + A + S +PH+ Sbjct: 286 MQKAKEAPAAAGATGGAGIPPIPA-VDFSKFGEVEEVALTRLMQVGAANLHRSWLNVPHV 344 Query: 223 TYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVI 282 T + D+T LE R + KLT+LP L++A + E P N++ I Sbjct: 345 TQFDSADITELEAFRVAQKAVAEKAGVKLTVLPLLLKACAFLLKELPDFNSSLAPSGKAI 404 Query: 283 HRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTI 342 R VHIG A TP GL VPV+++ + + + AAE LA+ ART + DE+ G+ Sbjct: 405 IRKKYVHIGFAVDTPDGLLVPVIKNVDQKSLLQLAAEAAALAEKARTKKLSADEMQGACF 464 Query: 343 TISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDG 402 TISSLG IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G Sbjct: 465 TISSLGHIGGTGFTPIVNAPEVAILGVSKATMQPVWDGKAFQPKLMLPLSLSYDHRVING 524 Query: 403 WDAAVFVQRLKTLL 416 AA F +RL +L Sbjct: 525 AAAARFTKRLGDVL 538 Score = 67.0 bits (162), Expect = 1e-15 Identities = 46/139 (33%), Positives = 68/139 (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--EGEIIELFVKVGDRIEADQSLLTLESDKASMEIPAPKAGVIKELKVKL 61 Query: 65 GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKP-AP 123 GD + L+ +E G A A PEA P A ++ A AP P AP Sbjct: 62 GDRLKEGDELLVLEAEGAAAAA-----PEA--------PAAAAAPAAAPAPAAEAAPAAP 108 Query: 124 KPAPAPREAPDLSAKPLAS 142 APA D+ + S Sbjct: 109 AAAPAAASVQDIHVPDIGS 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: 585 Number of extensions: 29 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: 546 Length adjustment: 34 Effective length of query: 392 Effective length of database: 512 Effective search space: 200704 Effective search space used: 200704 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