Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 7023193 Shewana3_0427 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase (RefSeq)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__ANA3:7023193 Length = 668 Score = 241 bits (616), Expect = 4e-68 Identities = 152/434 (35%), Positives = 232/434 (53%), Gaps = 35/434 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I++PD+G+ + +++E V GD + D L + TDKAT+E+P+P GK+L L +VG Sbjct: 239 IQVPDIGDA-SNVDVIEVLVSVGDMITADQGLITLETDKATMEVPAPFAGKLLSLTVKVG 297 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSI-PEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124 D V+ + + IET AP + P +A++ PVA + PP P P+ Sbjct: 298 DKVSQGSVIATIETVTAGAAPAPQAAAPAPVAQEAAPAPVAAAP----SRPPVPHHPSAG 353 Query: 125 PAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFI------- 177 AP + ASPAVR ARE G+DL QV G+G GRI ED+ ++ Sbjct: 354 -------APVATGVVHASPAVRRLAREFGVDLTQVTGSGRKGRIMKEDVQAYVKYELSRP 406 Query: 178 -SRGAEPLPAQTG------------LVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITY 224 + A + A G + VEE+ + +++ + + IPH+T Sbjct: 407 KATAATSVAAGNGGGLQVIAAPKVDFSKFGEVEEIPLSRIQKISGPNLHRNWVTIPHVTQ 466 Query: 225 VEEVDMTALEDLRATMN--RDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVI 282 +E D+T +E+ R N +K K+T L F+M+A+ KT+ + P N++ + Sbjct: 467 FDEADITEMEEFRKQQNDAAAKKKADYKITPLVFMMKAVAKTLQQFPVFNSSLSSDGESL 526 Query: 283 HRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTI 342 + HIG+A TP GL VPVVR + +GI + + EL ++ AR G ++ GS Sbjct: 527 IQKKYYHIGVAVDTPNGLVVPVVRDVDKKGIIELSRELADISIRARDGKLKSADMQGSCF 586 Query: 343 TISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDG 402 TISSLG IGG A TP++N+P+VAI+GV+K ++P W+G +F P+ ++ LS S+DHRVIDG Sbjct: 587 TISSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRVIDG 646 Query: 403 WDAAVFVQRLKTLL 416 AA F L +L Sbjct: 647 AMAARFSVTLSGIL 660 Score = 57.4 bits (137), Expect = 1e-12 Identities = 43/130 (33%), Positives = 65/130 (50%), Gaps = 11/130 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G G + ++E V GD + D L + TDKAT+++PSP G V + VG Sbjct: 126 VTVPDIG-GDTDVSVIEVLVAAGDKIEVDAGLITLETDKATMDVPSPFAGVVKEVKVAVG 184 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V+ + ++ +E G A AA P+A A PVA ++ A A P AP Sbjct: 185 DKVSQGSLVIMLEVGGAAPAAA---APQASA----SAPVAQAAPAAAVA---PVAAAPVV 234 Query: 126 APAPREAPDL 135 A + PD+ Sbjct: 235 AVKEIQVPDI 244 Score = 49.7 bits (117), Expect = 3e-10 Identities = 40/124 (32%), Positives = 59/124 (47%), Gaps = 23/124 (18%) Query: 8 MPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGDT 67 +PD+G E +++E GD + + + V +DKAT++IP+P G + L VGD Sbjct: 9 VPDIGGD--EVQVIEICASVGDTLAAEESILTVESDKATMDIPAPFAGVLAELKVAVGDK 66 Query: 68 VAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAP-PQPEKPAP-KP 125 V+ + ++ AG A A PVA +A AP P P PAP + Sbjct: 67 VSEGTLIAMMQAAGTANVQA--------------APVA-----QAAAPAPAPAAPAPVQA 107 Query: 126 APAP 129 APAP Sbjct: 108 APAP 111 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: 686 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: 668 Length adjustment: 35 Effective length of query: 391 Effective length of database: 633 Effective search space: 247503 Effective search space used: 247503 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