Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_048082312.1 EI99_RS12510 ketoisovalerate oxidoreductase
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000746075.1:WP_048082312.1 Length = 475 Score = 707 bits (1825), Expect = 0.0 Identities = 340/474 (71%), Positives = 402/474 (84%) Query: 1 MTKKVIRKPDSLHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISP 60 M +K+I+KP+S+ + FERKGGSAPTATHYC GCGHGILHKLIGEA+DEL I++R+V+ISP Sbjct: 1 MEEKIIKKPESILDTFERKGGSAPTATHYCPGCGHGILHKLIGEALDELEIEDRAVLISP 60 Query: 61 VGCAVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAA 120 VGCAVFAYYYFDCGNVQVAHGRAPAV TGI+RAED + +LYQGDGDLASIGLNETIQAA Sbjct: 61 VGCAVFAYYYFDCGNVQVAHGRAPAVATGITRAEDNAIAMLYQGDGDLASIGLNETIQAA 120 Query: 121 NRGEKMAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQA 180 NRGEK+AVFFVNNTVYGMTGGQMAPTTLIGEVTVTCP GRDPR+AGYPLHMCELLDNL A Sbjct: 121 NRGEKLAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPTGRDPRFAGYPLHMCELLDNLNA 180 Query: 181 PVFIERVSLADPKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLK 240 PVFIERVSL+D K IRKAK AVK+AL IQ++ KGYAFVE LSPCPTNLRQDA GAE+F+ Sbjct: 181 PVFIERVSLSDVKHIRKAKIAVKKALRIQKENKGYAFVEFLSPCPTNLRQDALGAEKFIN 240 Query: 241 EEMEREFPVKNFRDRSSETEPLIRSESDFSRESLDRIFQIKEDSVPDPVDDPEFREVRVK 300 EEME+EFP+K FRDR+ E EPL R +SDFS+ESL+++F I +S +++P+F E RVK Sbjct: 241 EEMEKEFPLKRFRDRTKEVEPLCRGKSDFSKESLNKLFNIGSESTGAAINNPDFGEKRVK 300 Query: 301 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 360 IAGFGGQGVLSMGLTLA+A + S+YPAYGPEQRGG+S+C V++SGE +GSP V+ Sbjct: 301 IAGFGGQGVLSMGLTLAEAGMKAQHYVSYYPAYGPEQRGGSSNCAVIMSGEVIGSPVVNE 360 Query: 361 PDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKENLRAIGVPALEIAKEHGTGRAA 420 DVLVA N+PSL+EF G+VR+GG+++YD++ F E + AI VPA +IAKEHG RA Sbjct: 361 VDVLVALNKPSLEEFVGEVRDGGLIIYDSSIGYFKAPEGIEAISVPAFKIAKEHGVKRAG 420 Query: 421 NTAMLGVMMALGITGLDEESFRDAIRFTFSGKDKIIDINLKILEAGADWARKNL 474 NT +LGV+MALG T L EE F+DAI+ TFS K K+I +NL+ILEAGA W R NL Sbjct: 421 NTVLLGVLMALGYTELPEEVFKDAIKHTFSKKPKLIPVNLEILEAGAKWVRDNL 474 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: 773 Number of extensions: 30 Number of successful extensions: 1 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: 475 Length adjustment: 33 Effective length of query: 445 Effective length of database: 442 Effective search space: 196690 Effective search space used: 196690 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: 51 (24.3 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