Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_015739363.1 ADEG_RS06990 MFS transporter
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000024605.1:WP_015739363.1 Length = 251 Score = 253 bits (645), Expect = 7e-72 Identities = 120/239 (50%), Positives = 161/239 (67%) Query: 15 VFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCG 74 +FER G HYC GC HGI+H+L+ E + EL + E++V + PVGCAVFAY YF+C Sbjct: 4 LFERTRGLTSKPFHYCPGCTHGIIHRLVAEVLVELDVLEKTVGVCPVGCAVFAYDYFNCD 63 Query: 75 NVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNT 134 ++ AHGRAPAV TG+ R VV YQGDGDLA+IG E + AA RGEK+ FVNN Sbjct: 64 MIEAAHGRAPAVATGVKRVLPDRVVFTYQGDGDLAAIGTAEIVHAAARGEKITTIFVNNA 123 Query: 135 VYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKS 194 +YGMTGGQMAPTTL+G+ T T P GR AGYPL + E+L ++ ++ RV++ PK+ Sbjct: 124 IYGMTGGQMAPTTLLGQKTTTTPFGRRAEEAGYPLRVAEMLATIEGAAYVARVAVNSPKN 183 Query: 195 IRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFR 253 + +AKR ++RA E+Q G G++ VEVLS CPTN A R+L+E+M +P+ F+ Sbjct: 184 VIQAKRVIRRAFEVQLAGLGFSLVEVLSTCPTNWGMSPPEALRWLEEKMIPVYPLGEFK 242 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: 308 Number of extensions: 12 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: 251 Length adjustment: 29 Effective length of query: 449 Effective length of database: 222 Effective search space: 99678 Effective search space used: 99678 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_015739362.1 ADEG_RS06985 2-oxoglutarate ferredoxin oxidoreductase subunit gamma
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000024605.1:WP_015739362.1 Length = 189 Score = 128 bits (322), Expect = 1e-34 Identities = 71/175 (40%), Positives = 107/175 (61%), Gaps = 4/175 (2%) Query: 299 VKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAV 358 V +AGFGGQG+LS G+ LAQA + G + +W P+YGPE RGGT++CGV +S + P V Sbjct: 5 VLLAGFGGQGILSAGMLLAQAGMAHGLYVAWIPSYGPEMRGGTANCGVTLSDRPISCPLV 64 Query: 359 DTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKENL--RAIGVPALEIAKEHGT 416 P L+A NQPSLD+FA V+ GG+++Y+++ A ++K+ L R +G+ A A+ G Sbjct: 65 TEPTTLLAMNQPSLDKFAPKVKPGGLIIYNSSLARWNKELGLGRRMLGLDATAQAEAIGN 124 Query: 417 GRAANTAMLGVMMALGITGLDEESFRDAIRFTF-SGKDKIIDINLKILEAGADWA 470 R A ++G +AL + E ++A+R + +I N K LE GA+ A Sbjct: 125 VRVAVNVLVGAFIAL-TQIIPLEKAKEALRVVLPPHRHHLIAANEKALEVGANLA 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: 217 Number of extensions: 6 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: 189 Length adjustment: 26 Effective length of query: 452 Effective length of database: 163 Effective search space: 73676 Effective search space used: 73676 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