Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Pf6N2E2_3675 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3675 Length = 545 Score = 257 bits (656), Expect = 7e-73 Identities = 163/431 (37%), Positives = 227/431 (52%), Gaps = 34/431 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 121 IHVPDIGSS-GKAKIIEVLVKAGDTVEADQSLITLESDKASMEIPSPAAGVVESVEIKLE 179 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V +++++ AG A AAP + A +++ EA P PA K Sbjct: 180 DEVGTGDLILKLKVAGAAAPAAPA------------QAAAPAAKTEAAPAPAAAAPAAKA 227 Query: 126 --APAPREAPDLS-AKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR--- 179 APAP AP S AK A PAVR ARE G++L V +GP GR+ ED+ ++ Sbjct: 228 EAAPAPAAAPAPSGAKVHAGPAVRQLAREFGVELSAVGPSGPHGRVLKEDVQAYVKAMMQ 287 Query: 180 --------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYV 225 G P+PA R EEV M L + A + S IPH+T Sbjct: 288 KAKNAPAEGATGGAGIPPIPA-VDFSRFGETEEVAMTRLMQIGASSLHRSWLNIPHVTQF 346 Query: 226 EEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRH 285 ++ D+T LE R + KLT+LP L++A + E P NA+ + R Sbjct: 347 DQADITELEAFRVAQKAVAEKAGVKLTVLPLLLKACAHLLKELPDFNASLAPSGKAVIRK 406 Query: 286 AAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITIS 345 VHIG A TP GL VPV+R+ + + + AAE LA+ AR T D++ G+ TIS Sbjct: 407 KYVHIGFAVDTPEGLLVPVIRNVDQKSLLQLAAEAAALAEKARNKKLTADDMQGACFTIS 466 Query: 346 SLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDA 405 SLG IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G A Sbjct: 467 SLGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAA 526 Query: 406 AVFVQRLKTLL 416 A F +RL LL Sbjct: 527 ARFTKRLSDLL 537 Score = 68.6 bits (166), Expect = 5e-16 Identities = 43/138 (31%), Positives = 69/138 (50%), Gaps = 13/138 (9%) Query: 5 IIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEV 64 +I++PD+G G E E++E VK GD + D + + +DKA++E+P+P G + L ++ Sbjct: 4 LIRVPDIGSG--EGEVIELFVKVGDRIEADQSILTLESDKASMEVPAPKAGVIKSLKVKL 61 Query: 65 GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124 GD + L+ +E G A AAP++ A A ++ A AP PAP Sbjct: 62 GDRLKEGDELLELEVEGAA--AAPEAAAPA---------AAPAAEKPAAAPAAEAAPAPA 110 Query: 125 PAPAPREAPDLSAKPLAS 142 APA D+ + S Sbjct: 111 AAPAAATVQDIHVPDIGS 128 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: 581 Number of extensions: 27 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: 545 Length adjustment: 34 Effective length of query: 392 Effective length of database: 511 Effective search space: 200312 Effective search space used: 200312 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