Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF434 PS417_02215 dihydrolipoamide acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__WCS417:GFF434 Length = 548 Score = 255 bits (652), Expect = 2e-72 Identities = 164/430 (38%), Positives = 228/430 (53%), Gaps = 30/430 (6%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I +PD+G +A+++E VK GD V D L + +DKA++EIPSP G V + ++ Sbjct: 122 IHVPDIGSS-GKAKIIELLVKVGDTVEADQSLITLESDKASMEIPSPAAGVVESIAVKLE 180 Query: 66 DTVAVKAPLVRIETAGEAGEAAPD--SIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAP 123 D V +++++ G A AAP + P A AE P A + AKA P A Sbjct: 181 DEVGTGDFILKLKVQGAAPAAAPAPAAAPAAKAEAA---PAAAAPAPAAKAEAAPAPAAA 237 Query: 124 KPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFIS---RG 180 PAP+ AK A PAVR ARE G++L V+ TGP GR+ ED+ +++ + Sbjct: 238 APAPS-------GAKVHAGPAVRQLAREFGVELSAVSATGPHGRVLKEDVQVYVKAMMQK 290 Query: 181 AEPLPAQTGLV--------------RKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226 A+ PA G R +EEV M L + A + S IPH+T + Sbjct: 291 AKEAPAAGGATGGSGIPPIRTVDFSRFGEIEEVPMTRLMQIGAAGLHASWLNIPHVTQFD 350 Query: 227 EVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHA 286 + D+T LE R + KLT+LP L++A + E P NA+ I R Sbjct: 351 QADITDLEAFRVAQKAVAEKAGVKLTVLPLLLKACAHLLKELPDFNASLAPSGKAIIRKK 410 Query: 287 AVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISS 346 VHIG A TP GL VPV+++ + + + AAE LA AR T D++ G+ TISS Sbjct: 411 YVHIGFAVDTPDGLLVPVIKNVDQKSLLQLAAEAAALAAKARDKKLTPDDMQGACFTISS 470 Query: 347 LGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAA 406 LG IGG TP++N PEVAI+GV+K ++PVWDG F P+ ++ LS S+DHRVI+G AA Sbjct: 471 LGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAA 530 Query: 407 VFVQRLKTLL 416 F QRL LL Sbjct: 531 RFTQRLSQLL 540 Score = 70.1 bits (170), Expect = 2e-16 Identities = 46/129 (35%), Positives = 67/129 (51%), Gaps = 18/129 (13%) Query: 5 IIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEV 64 +I++PD+G G E E++E VK GD V D + + +DKA++EIP+P G V L ++ Sbjct: 4 LIRVPDIGSG--EGEVIELFVKVGDTVEADQSILTLESDKASMEIPAPKAGVVKSLKVKL 61 Query: 65 GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124 GD + L+ +E G A +AAP + P A A A AP + A + Sbjct: 62 GDRLKEGDELLELEIEG-AADAAPAAAPAAAA---------------APAPAAEKPAAAE 105 Query: 125 PAPAPREAP 133 APAP AP Sbjct: 106 AAPAPAAAP 114 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: 593 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: 548 Length adjustment: 34 Effective length of query: 392 Effective length of database: 514 Effective search space: 201488 Effective search space used: 201488 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