Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate PfGW456L13_215 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_215 Length = 653 Score = 242 bits (618), Expect = 2e-68 Identities = 156/430 (36%), Positives = 221/430 (51%), Gaps = 32/430 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 229 IHVPDIGSA-GKAKIIEVLVKAGDTVVADQSLITLESDKASMEIPSPAAGVVESVSIKLD 287 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V +++++ G A A + A A A S+ A A P PA P Sbjct: 288 DEVGTGDLILKLKVKGAAPAAPVAATAPAAA--------APSAPAPAAAAPAAAAPAAAP 339 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179 AP + AK A PAVR ARE G++L V +GP GRI ED+ +++ Sbjct: 340 VAAPAKP---GAKVHAGPAVRQLAREFGVELSAVGASGPHGRILKEDVQVYVKAMMQKAK 396 Query: 180 -------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226 G P+P R +EEV M L + A + S +PH+T + Sbjct: 397 EAPAAAAGASGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQVGAANLHRSWLNVPHVTQFD 455 Query: 227 EVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHA 286 D+T LE R + KLTILP L++ + E P N++ I R Sbjct: 456 SADITELEAFRVAQKAVAEKAGVKLTILPLLLKTCAHLLKELPDFNSSLAPSGKAIIRKK 515 Query: 287 AVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISS 346 V+IG A TP GL VPV+++ + + + AAE LA+ ART + DE+ G+ TISS Sbjct: 516 YVNIGFAVDTPDGLLVPVIKNVDQKSLLQLAAEAASLAEKARTKKLSSDEMQGACFTISS 575 Query: 347 LGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAA 406 LG IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G AA Sbjct: 576 LGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAA 635 Query: 407 VFVQRLKTLL 416 F +RL LL Sbjct: 636 RFTKRLSDLL 645 Score = 63.9 bits (154), Expect = 1e-14 Identities = 37/112 (33%), Positives = 60/112 (53%), Gaps = 5/112 (4%) 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 GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPP 116 GD + L+ +E G A A + P A AE +P A + A A P Sbjct: 62 GDRLKEGDELLELEVEGAAAAAPAAAAPAAKAEA---KPAAAPAAAPAPAAP 110 Score = 62.8 bits (151), Expect = 3e-14 Identities = 45/148 (30%), Positives = 65/148 (43%), Gaps = 30/148 (20%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 118 VHVPDIGSS-GKAQIIEIQVKVGDTVAADQSLITLESDKASMEIPSPAAGVVKAISVKLN 176 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V ++ +E AG A AA AP Q PAP Sbjct: 177 DEVGTGDLILDLEVAGAAAPAA--------------------------APAQAAAPAPAA 210 Query: 126 APAPREAPDLSAKPLASPAVRLRARESG 153 APA AP A P+A + + G Sbjct: 211 APAAAAAP---AAPVADSVQDIHVPDIG 235 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: 726 Number of extensions: 34 Number of successful extensions: 7 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: 653 Length adjustment: 35 Effective length of query: 391 Effective length of database: 618 Effective search space: 241638 Effective search space used: 241638 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