Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 3608573 Dshi_1967 catalytic domain of components of various dehydrogenase complexes (RefSeq)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Dino:3608573 Length = 433 Score = 238 bits (608), Expect = 2e-67 Identities = 151/429 (35%), Positives = 225/429 (52%), Gaps = 35/429 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G+ + +V V GD V E+ L + +DKAT+E+PSPV GKV+ + G Sbjct: 14 VNVPDIGD-FTDVPVVSILVSVGDVVAEEDPLLELESDKATMEVPSPVAGKVVEIKVAEG 72 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 DTV+ + L+ + A + A + P A A A AP P AP Sbjct: 73 DTVS-EGTLIMMMEAEDGAAGASEPAPSAPA---------------ASAPAAPSAAAPAA 116 Query: 126 APAPREAPDLSA---KPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISRGAE 182 P+ AP A K ASP+VR AR IDL +V GTG GRI ED+ ++ Sbjct: 117 PTDPKPAPVTDAGFGKAHASPSVRAFARSLEIDLSKVNGTGRKGRILREDVTAYLKSSTA 176 Query: 183 PLPAQTGLV---------------RKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEE 227 P PA+ G + VE+V M +++ + S IPH+T+ +E Sbjct: 177 PAPAKGGAASGGMGIPPIPVVDFSKFGPVEDVEMPRIKKISGPALHRSWLNIPHVTHNDE 236 Query: 228 VDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAA 287 D+T L+ R M+ K + ++T+L F+++A V + N++ + + A Sbjct: 237 ADITDLDKYRKEMDTQAKEDGYRVTLLSFVIKASVSALKTHWEFNSSIHPDGDKLIKKAF 296 Query: 288 VHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSL 347 +IG A TP GL VPV++ A+ +G+ + + EL L+ AR G ++ G+T TISSL Sbjct: 297 YNIGFAADTPNGLMVPVIKDADRKGLVEISKELMELSAKARAGELKGPDMQGATFTISSL 356 Query: 348 GAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAV 407 G IGG + TP++N PEVAI+G+ + + PVW+G +FVPR + LS S+DHR +DG AA Sbjct: 357 GGIGGTSFTPIVNAPEVAILGLTRSKMAPVWNGEEFVPRLMQPLSLSYDHRAVDGALAAR 416 Query: 408 FVQRLKTLL 416 F LKTLL Sbjct: 417 FCVTLKTLL 425 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: 442 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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: 51 (24.3 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