Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_035238982.1 Q366_RS11415 2-oxoglutarate oxidoreductase
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000745975.1:WP_035238982.1 Length = 247 Score = 237 bits (605), Expect = 3e-67 Identities = 114/240 (47%), Positives = 154/240 (64%), Gaps = 10/240 (4%) Query: 4 KVIRKPDSLHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGC 63 K KP++L + + THYC GC HGI+H+L+ EAIDELGI+E +V I+PVGC Sbjct: 3 KAFSKPEALTDNY----------THYCPGCTHGIVHRLVAEAIDELGIRENTVGIAPVGC 52 Query: 64 AVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRG 123 AV Y Y +C + AHGRAPA+ TGI R +V YQGDGDLASIG+ E I AANRG Sbjct: 53 AVMIYDYINCDFQEAAHGRAPAMATGIKRVRPDLMVFTYQGDGDLASIGMGEIIHAANRG 112 Query: 124 EKMAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVF 183 EK+ V F+NN +YGMTGGQMAPTT+ G+ T P GRD G P+ M L+ + P + Sbjct: 113 EKITVIFINNAIYGMTGGQMAPTTMPGQRATTAPAGRDTAQTGMPIRMANLMSEIVTPGY 172 Query: 184 IERVSLADPKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEM 243 + R ++ P+ + K K+A+K+A + Q D ++FVEV+S CPTN A ++ +E + Sbjct: 173 VTRQAVLKPQMVNKCKKAIKKAFQYQMDNTCFSFVEVVSTCPTNWGMTPINALKWAEETL 232 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: 339 Number of extensions: 18 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: 247 Length adjustment: 29 Effective length of query: 449 Effective length of database: 218 Effective search space: 97882 Effective search space used: 97882 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_035238983.1 Q366_RS11420 2-oxoacid:ferredoxin oxidoreductase subunit gamma
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000745975.1:WP_035238983.1 Length = 178 Score = 121 bits (304), Expect = 2e-32 Identities = 66/172 (38%), Positives = 101/172 (58%), Gaps = 2/172 (1%) Query: 296 EVRVKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGS 355 + +K AGFGGQG+L LA AA +G +W P+YGPE RGGT+ C VVIS + +GS Sbjct: 2 QTEIKFAGFGGQGILLSAKLLAYAAMKQGFQVAWIPSYGPEMRGGTAYCTVVISDKLIGS 61 Query: 356 PAVDTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADF-SKKENLRAIGVPALEIAKEH 414 P + +P LVA N+PSL++F ++ GGIV + + S+++++ + VP +IA E Sbjct: 62 PIIKSPTHLVAMNRPSLEKFDDTIKPGGIVFINASLIPVRSQRKDVVELVVPVNDIAIEA 121 Query: 415 GTGRAANTAMLGVMMALGITGLDEESFRDAIRFTFSGKDKIIDINLKILEAG 466 G+ RAAN L A +D + + ++ F+ K KII +N+ + G Sbjct: 122 GSVRAANIVALAAFAAKSKL-VDLDLLKKCVKEEFAAKAKIIPLNMDAFDRG 172 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: 178 Number of extensions: 6 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: 178 Length adjustment: 26 Effective length of query: 452 Effective length of database: 152 Effective search space: 68704 Effective search space used: 68704 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: 47 (22.7 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