Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF3102 HP15_3045 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Marino:GFF3102 Length = 554 Score = 261 bits (668), Expect = 3e-74 Identities = 156/427 (36%), Positives = 232/427 (54%), Gaps = 23/427 (5%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 +K+P + +G ++E +V GD + D L V +DKAT+EIPSP +GKV + G Sbjct: 127 VKVPAL-DGFDNVPVIEINVAEGDTIEADDPLVTVESDKATMEIPSPYSGKVGKILVSEG 185 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIP--EALAEQVLDEPVAVSSRLEAKAPPQPEKPAP 123 D ++ L+ + E GEA DS P E A++ EP + + P Q + AP Sbjct: 186 DKLSEGHELLEMTVQEEGGEAEDDSEPASEEPAKEEKSEPKS------EEKPKQQAESAP 239 Query: 124 KPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISRGAEP 183 +P A E P AK A PAVR ARE G DL ++ G+GP RI +D+ ++ + Sbjct: 240 EPQGATYEPPTPGAKVHAGPAVRKLARELGADLARIKGSGPKSRIIKDDVHAYVKSQLKQ 299 Query: 184 LPAQTGLVRKTAVEEVRMIG------LRRRIAEKMSLSTSR--------IPHITYVEEVD 229 +G+ + + V++ ++R +M +T+ +PH+T E+ D Sbjct: 300 AQQGSGVATGSGIPGVKLPDFSQFGEVKREAMSRMMFATANNMQRSWLNVPHVTQFEDAD 359 Query: 230 MTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAVH 289 +T +ED R + + K+T LPFL++A +AE P N + D + R +H Sbjct: 360 ITDMEDFRKAQKAAGEKKGVKMTPLPFLLKACATALAELPQFNVSLDMERKEVVRKKYIH 419 Query: 290 IGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLGA 349 IGIA TP GL VPV++ + +G+W+ AAE LA AR E+ G+ TI+SLG Sbjct: 420 IGIAVDTPNGLMVPVIKDVDKKGLWELAAESAELAQKARDKQLKPAEMQGACFTITSLGG 479 Query: 350 IGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVFV 409 IGG A TP++N PEVAI+GV+K A++PVWDG +F PR ++ LS S+DHR ++G DAA F Sbjct: 480 IGGTAFTPIVNTPEVAILGVSKAAMKPVWDGKEFQPRLMLPLSLSYDHRAVNGADAARFT 539 Query: 410 QRLKTLL 416 L LL Sbjct: 540 TVLSQLL 546 Score = 63.5 bits (153), Expect = 2e-14 Identities = 46/128 (35%), Positives = 66/128 (51%), Gaps = 12/128 (9%) Query: 1 MGEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWL 60 M E IK+PD+G G E E++E V GD V + + V +DKA+VE+PSP GK+ + Sbjct: 1 MSEQEIKVPDLG-GADEVEVIEITVSAGDSVEAEDPILTVESDKASVELPSPGAGKITKI 59 Query: 61 GAEVGDTVAVKAPLVRIETAGEAGEAAPDS--IPEALAEQVLDEPVAVSSRLEAKAPPQP 118 +VGD V + +V + A G + DS PE AE+ S + + + Sbjct: 60 TVKVGDKVK-EGDVVGMMEASADGGGSDDSEEEPEGKAEE--------KSEADKQEKSEE 110 Query: 119 EKPAPKPA 126 KPAPK A Sbjct: 111 SKPAPKKA 118 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: 544 Number of extensions: 21 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: 554 Length adjustment: 34 Effective length of query: 392 Effective length of database: 520 Effective search space: 203840 Effective search space used: 203840 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