Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate N515DRAFT_2156 N515DRAFT_2156 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Dyella79:N515DRAFT_2156 Length = 562 Score = 246 bits (627), Expect = 2e-69 Identities = 160/431 (37%), Positives = 233/431 (54%), Gaps = 25/431 (5%) Query: 7 KMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGD 66 ++PD+G G ++E VK GD V +D L + +DKAT+E+P+P G V L +VGD Sbjct: 128 RVPDIG-GHDGVPVIEVLVKVGDTVAKDQSLITLESDKATMEVPAPFGGVVKELKVKVGD 186 Query: 67 TVAVKAPLVRIETAGEAGEAAPDSIP-EALAEQVLDEPVAVSSR--LEAKAPPQPEKPAP 123 ++ A + IE+A A AAP P +A QV ++P + R L AP PA Sbjct: 187 ELSEGAVIALIESADGAPAAAPAPAPAKAEVPQVEEKPAPIGGRGILPGNAPEGDVAPAA 246 Query: 124 KPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR---- 179 +P R A P ASPA+R ARE G+D+RQ G+G GRI ED+ ++ Sbjct: 247 RPPFDSRIVMPGDA-PYASPAIRAFARELGVDIRQAKGSGRGGRIVREDITSYVKHALAS 305 Query: 180 GAEPL----PAQTGL----------VRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYV 225 GA P PA GL + +EE + +++ ++ + + IPH+T Sbjct: 306 GARPSGAAQPAGGGLNLLPWPKVDFAKFGPIEEKPLTRIQKISGANLARNWAMIPHVTQH 365 Query: 226 EEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRH 285 E+ D+T LE R + + K K+T L F ++A+V + + P NA+ D+ + Sbjct: 366 EDADITELEAFRKKLGEENK--DLKITPLVFQIKAVVAALKKFPQFNASLDETGEKLILK 423 Query: 286 AAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITIS 345 H+GIA TP GL VPV+R + +G+ D A EL ++ AR ++++G +IS Sbjct: 424 KYFHVGIAVDTPDGLVVPVIRDCDKKGLLDLAVELGEISKKARDKKLGPNDMSGGCFSIS 483 Query: 346 SLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDA 405 SLG IGG A TP++N PEVAI+GV+K +PVW+G +F PR I+ LS S+DHRVIDG A Sbjct: 484 SLGGIGGTAFTPIVNAPEVAILGVSKAQTKPVWNGKEFAPRLILPLSLSYDHRVIDGALA 543 Query: 406 AVFVQRLKTLL 416 A F L L Sbjct: 544 ARFAAFLANQL 554 Score = 64.7 bits (156), Expect = 7e-15 Identities = 50/148 (33%), Positives = 72/148 (48%), Gaps = 26/148 (17%) Query: 7 KMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGD 66 ++PD+G ++E VKPGD V ++ L + +DKAT+E+P+P G V + +VGD Sbjct: 8 RVPDIGHD--NVPVIEVLVKPGDKVAKEQGLVTLESDKATMEVPAPFAGTVKEVKLKVGD 65 Query: 67 TVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKPA 126 V+ A + IE A EA +AP P+A A P P AP PA Sbjct: 66 EVSEGAVIAIIE-ADEA--SAPAPAPQA-------------------AAPAPAPAAPAPA 103 Query: 127 PAPREAPDLSAKPLASPAVRLRARESGI 154 PA P +A P +PA RE+ + Sbjct: 104 PAKAAEPTRAAAP--APAAGGGVREARV 129 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: 616 Number of extensions: 31 Number of successful extensions: 7 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: 562 Length adjustment: 34 Effective length of query: 392 Effective length of database: 528 Effective search space: 206976 Effective search space used: 206976 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