Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Pf1N1B4_1477 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1477 Length = 655 Score = 244 bits (623), Expect = 6e-69 Identities = 160/430 (37%), Positives = 222/430 (51%), Gaps = 34/430 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 233 IHVPDIGSA-GKAKIIEVLVKAGDTVVADQSLITLESDKASMEIPSPAAGVVESVSIKLD 291 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V +++++ G A AAP P A A P A + A AP P AP Sbjct: 292 DEVGTGDLILKLKVKGAAPAAAP--APAAAA------PSAPAPAPAAAAPAAPAPAAPVA 343 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179 APA AK A PAVR ARE G++L V +GP GRI ED+ +++ Sbjct: 344 APAKP-----GAKVHAGPAVRQLAREFGVELSAVGASGPHGRILKEDVQVYVKAMMQKAK 398 Query: 180 -------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226 G P+P R +EEV M L + A + S IPH+T + Sbjct: 399 EAPTAAAGATGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQIGASSLHRSWLNIPHVTQFD 457 Query: 227 EVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHA 286 D+T LE R + KLTILP L+++ + E P N++ I R Sbjct: 458 SADITELEAFRIAQKAVAEKAGVKLTILPLLLKSCAHLLKELPDFNSSLAPSGKAIIRKK 517 Query: 287 AVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISS 346 V+IG A TP GL VPV+++ + + + AAE LA AR T D++ G+ TISS Sbjct: 518 YVNIGFAVDTPEGLLVPVIKNVDQKSLLQLAAEAAALAAKARDKKLTADDMQGACFTISS 577 Query: 347 LGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAA 406 LG IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G AA Sbjct: 578 LGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAA 637 Query: 407 VFVQRLKTLL 416 F +RL LL Sbjct: 638 RFTKRLSDLL 647 Score = 62.8 bits (151), Expect = 3e-14 Identities = 41/128 (32%), Positives = 64/128 (50%), Gaps = 15/128 (11%) Query: 5 IIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEV 64 +I++PD+G G E E++E VK GD + D + + +DKA++E+P+P G + L ++ Sbjct: 4 LIRVPDIGSG--EGEVIELFVKVGDRIEADQSILTLESDKASMEVPAPKAGIIKSLKVKL 61 Query: 65 GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124 GD + L+ +E G A A P A A A + +A+A P K Sbjct: 62 GDRLKEGDELLELEVEGAAAPA-----PAAAA--------AAAPAAKAEAAPAAAKAPAA 108 Query: 125 PAPAPREA 132 PA AP A Sbjct: 109 PAAAPAAA 116 Score = 58.9 bits (141), Expect = 4e-13 Identities = 37/113 (32%), Positives = 55/113 (48%), Gaps = 8/113 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 121 VHVPDIGSS-GKAQIIEIQVKVGDTVEADQSLITLESDKASMEIPSPAAGVVKAISVKLN 179 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQP 118 D V ++ +E AG A P A A P A + A AP P Sbjct: 180 DEVGTGDLILDLEVAGAAA-------PAAAAPAQAAAPAAAAPAPAAAAPAAP 225 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: 731 Number of extensions: 33 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: 3 Length of query: 426 Length of database: 655 Length adjustment: 35 Effective length of query: 391 Effective length of database: 620 Effective search space: 242420 Effective search space used: 242420 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