Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Ga0059261_2271 Ga0059261_2271 branched-chain alpha-keto acid dehydrogenase E2 component (EC 2.3.1.168)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Korea:Ga0059261_2271 Length = 427 Score = 409 bits (1052), Expect = e-119 Identities = 224/430 (52%), Positives = 291/430 (67%), Gaps = 8/430 (1%) Query: 1 MGEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWL 60 M F ++PD+GEG+AEAE+V WHVK GD V ED +A +MTDKATVE+ SPV+G V+ L Sbjct: 1 MARFTFRLPDIGEGIAEAEIVAWHVKVGDRVEEDQQVADMMTDKATVEMESPVSGIVVEL 60 Query: 61 GAEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAP-PQPE 119 EVGD VA+ A L+ +ET G+A E+ P++ P A + P AV + +AP P Sbjct: 61 AGEVGDQVAIGAALIVVETDGDAAES-PEAAPALEAVEAPPAPPAVEPPVAPEAPVAPPA 119 Query: 120 KPAPKPAPAPREAPDLSAKP----LASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDL 175 PAP PAPAP A P LASPAVR RA++ GIDL QV RI H DLD Sbjct: 120 PPAPPPAPAPEPVAAAPAAPHRDILASPAVRQRAKDLGIDLSQVKAA-EGDRIRHADLDA 178 Query: 176 FISRGAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEVDMTALED 235 F+ G+ R V++IG+RR+IAE M+ S IPH TYV+E+D+TALE+ Sbjct: 179 FLRYGSAQGYHAPHASRAREDVPVKVIGMRRKIAENMAASKRAIPHFTYVDEIDVTALEE 238 Query: 236 LRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAVHIGIATQ 295 +RA +N +R + KLT+LPF++ A+ +T+ + P +NA +DD AGV+ RH VH+G+ATQ Sbjct: 239 MRADLNANRGA-RPKLTMLPFVIAAICRTLPDFPMLNARYDDEAGVVTRHGRVHMGMATQ 297 Query: 296 TPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLGAIGGIAS 355 T AGL VPV+R A+ +W AAE+ RLA+AARTG A +EL+GSTITI+SLG +GGIA+ Sbjct: 298 TDAGLMVPVIRDAQDLNVWQLAAEITRLAEAARTGKAKVEELSGSTITITSLGPLGGIAT 357 Query: 356 TPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVFVQRLKTL 415 TPVIN PEVAI+G NKI RPV+ G V K+MNLS S DHRV+DGWDAA +VQ L+ L Sbjct: 358 TPVINKPEVAIIGPNKIVERPVFVGDDIVRAKLMNLSISCDHRVVDGWDAASYVQALRKL 417 Query: 416 LETPALIFVE 425 LETP L+F + Sbjct: 418 LETPVLLFAD 427 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: 527 Number of extensions: 17 Number of successful extensions: 5 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: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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