Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_018124182.1 B149_RS0105545 MFS transporter
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000375485.1:WP_018124182.1 Length = 255 Score = 254 bits (649), Expect = 2e-72 Identities = 121/240 (50%), Positives = 162/240 (67%) Query: 15 VFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCG 74 VF+R THYC GC HG+ H+++GE +DELG++E S+++S +GC+VF Y Y + Sbjct: 9 VFDRPESVIDRPTHYCPGCHHGVAHRMVGELLDELGLRENSILVSSIGCSVFLYNYLNVD 68 Query: 75 NVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNT 134 V+ HGRAPAV TG+ A V YQGDGDLASIG+ E + AANRGEK++V FVNNT Sbjct: 69 AVEAPHGRAPAVATGVKAARKDNFVFAYQGDGDLASIGMAEILHAANRGEKISVVFVNNT 128 Query: 135 VYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKS 194 VYGMTGGQMAPTTLIG+ T TCP GR + G P+ M E++ +L F R SL + K+ Sbjct: 129 VYGMTGGQMAPTTLIGQRTTTCPSGRCLEHEGAPIRMTEIISSLGGTAFAARGSLDNVKN 188 Query: 195 IRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFRD 254 IR AK+ +++A E Q GKG+ FVE+LS CPTN + D + ++ EM FP+ ++D Sbjct: 189 IRTAKKYMRKAFECQTQGKGFGFVELLSACPTNWKMDPIKSNERIQTEMIPYFPLGVYKD 248 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: 360 Number of extensions: 13 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: 255 Length adjustment: 29 Effective length of query: 449 Effective length of database: 226 Effective search space: 101474 Effective search space used: 101474 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: 49 (23.5 bits)
Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_018124181.1 B149_RS0105540 2-oxoacid:ferredoxin oxidoreductase subunit gamma
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000375485.1:WP_018124181.1 Length = 181 Score = 112 bits (279), Expect = 1e-29 Identities = 65/173 (37%), Positives = 101/173 (58%), Gaps = 8/173 (4%) Query: 301 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 360 IAGFGGQGV+ +G LA A +G + ++ P YGPE RGGT++C VV++ E +GSP + Sbjct: 9 IAGFGGQGVMLIGNLLAYAGMQDGLNVTYIPVYGPEMRGGTANCTVVLAEEEIGSPIIRR 68 Query: 361 PDVLVAFNQPSLDEFAGDVREGGIVLYDTATAD--FSKKENLRAIGVPALEIAKEHGTGR 418 P L+ N+PSLD+F +++ GI + +++ D + + L + VPA +IA + G R Sbjct: 69 PTSLIIMNRPSLDKFQSRLQDDGICVVNSSLVDMELADTDRLNCLAVPANDIADKLGNTR 128 Query: 419 AANTAMLGV-MMALGITGLD--EESFRDAIRFTFSGKDKIIDINLKILEAGAD 468 AN LG + A + LD + + + I +S +I N + L+AGAD Sbjct: 129 MANMVALGAFIQATQVMPLDVVQGALENVISAHYS---HLIPKNAEALQAGAD 178 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: 174 Number of extensions: 7 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: 181 Length adjustment: 26 Effective length of query: 452 Effective length of database: 155 Effective search space: 70060 Effective search space used: 70060 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: 48 (23.1 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