Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_048060885.1 MTH_RS03300 ketoisovalerate oxidoreductase
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000008645.1:WP_048060885.1 Length = 490 Score = 880 bits (2273), Expect = 0.0 Identities = 431/477 (90%), Positives = 461/477 (96%), Gaps = 1/477 (0%) Query: 1 MTKKVIRKPDSLHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISP 60 +TKKVIRKPDSLH+VFERKGGSAPTATHYCAGCGHGILHKLIGEA+DELGIQER+VMISP Sbjct: 14 VTKKVIRKPDSLHDVFERKGGSAPTATHYCAGCGHGILHKLIGEAMDELGIQERAVMISP 73 Query: 61 VGCAVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAA 120 VGCAVFAYYYFDCGNVQVAHGRAPAVGTGISRAED VV+LYQGDGDLASIGLNETIQAA Sbjct: 74 VGCAVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDDAVVILYQGDGDLASIGLNETIQAA 133 Query: 121 NRGEKMAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQA 180 NRGEK+AVFFVNNTVYGMTGGQMAPTTL+GEVTVTCP GRDPRYAGYPLHMCELLDNLQA Sbjct: 134 NRGEKLAVFFVNNTVYGMTGGQMAPTTLVGEVTVTCPTGRDPRYAGYPLHMCELLDNLQA 193 Query: 181 PVFIERVSLADPKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLK 240 PVFIERVSLADPK IR+A+RA+KRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLK Sbjct: 194 PVFIERVSLADPKRIRRARRAIKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLK 253 Query: 241 EEMEREFPVKNFRDRSSETEPLIRSESDFSRESLDRIFQIKEDSVPDPVDDPEFREVRVK 300 EEME+EFPVKNFRDRS+ETEPLIRSESDFSRESLDRIFQI+EDSVPDPVDDPEF EVRVK Sbjct: 254 EEMEKEFPVKNFRDRSAETEPLIRSESDFSRESLDRIFQIREDSVPDPVDDPEFPEVRVK 313 Query: 301 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 360 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT Sbjct: 314 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 373 Query: 361 PDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKENLRAIGVPALEIAKEHGTGRAA 420 PDVLVA NQPSLDEFA DV +GGI+LYD+ TA FS +RA+GVPALEIA++HGT RAA Sbjct: 374 PDVLVALNQPSLDEFADDVADGGIILYDSTTASFSGGA-VRAMGVPALEIARKHGTARAA 432 Query: 421 NTAMLGVMMALGITGLDEESFRDAIRFTFSGKDKIIDINLKILEAGADWARKNLEGE 477 NT MLGVMMALG+TGLDEESFR+AI+FTF+GK+KIID+NL+ILEAGA+WAR+N+EGE Sbjct: 433 NTVMLGVMMALGLTGLDEESFREAIKFTFAGKEKIIDMNLRILEAGAEWARENIEGE 489 Lambda K H 0.318 0.137 0.402 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: 921 Number of extensions: 30 Number of successful extensions: 2 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: 478 Length of database: 490 Length adjustment: 34 Effective length of query: 444 Effective length of database: 456 Effective search space: 202464 Effective search space used: 202464 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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