Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_092053449.1 BQ4888_RS02180 2-oxoglutarate oxidoreductase
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_900111775.1:WP_092053449.1 Length = 247 Score = 247 bits (630), Expect = 4e-70 Identities = 123/246 (50%), Positives = 160/246 (65%) Query: 12 LHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYF 71 + +VF TH+C GC HG +H+L+ EA+D G+QE+++ ++ VGC+VF Y YF Sbjct: 1 MQQVFAHPVSLKDVQTHFCPGCQHGTIHRLVAEAMDHFGVQEKTIGVASVGCSVFLYGYF 60 Query: 72 DCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFV 131 D V+ HGRAPAV TG+ RA VV YQGDGDLA+IG +E I AANRGE M V FV Sbjct: 61 DIDVVEAPHGRAPAVATGVKRACPDKVVFTYQGDGDLAAIGTSEIIHAANRGEGMTVIFV 120 Query: 132 NNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLAD 191 NNT YGMTGGQMAPTTL + T T P GR+ GYP+ M ELL L+ + RV++ Sbjct: 121 NNTTYGMTGGQMAPTTLPSQKTSTSPYGRNVANDGYPIRMAELLAQLEGVAYSARVAVNT 180 Query: 192 PKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKN 251 PK++ +A R +K+A E Q G+G++FVEVLS CPTN D A + EEM FP+ Sbjct: 181 PKNVVQAGRVIKQAFETQIQGRGFSFVEVLSACPTNWGMDPLKANARIGEEMIPYFPLAI 240 Query: 252 FRDRSS 257 F+D S+ Sbjct: 241 FKDTSA 246 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: 332 Number of extensions: 11 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_092053047.1 BQ4888_RS02175 2-oxoacid:ferredoxin oxidoreductase subunit gamma
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_900111775.1:WP_092053047.1 Length = 186 Score = 110 bits (274), Expect = 5e-29 Identities = 65/178 (36%), Positives = 103/178 (57%), Gaps = 8/178 (4%) Query: 299 VKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAV 358 V +AGFGGQG+L +G LA AA EGR+TS++PAYG E+RGG ++C VV++ VGSP + Sbjct: 5 VFMAGFGGQGILLIGNLLAYAAIREGRNTSYFPAYGVEKRGGAATCTVVVADGEVGSPVI 64 Query: 359 DTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFS--KKENLRAIGVPALEIAKEHGT 416 P + N S++++ G VR GG+ + +++ + S + +LR + +P E+A E G Sbjct: 65 GNPGAAILLNPLSMEKYFGRVRAGGLCIVNSSLIEESGDGRSDLRVLRLPLNELALEIGD 124 Query: 417 GRAANTAMLGVMMAL-GITGLD--EESFRDAIRFTFSGKDKIIDINLKILEAGADWAR 471 R N +G L G LD + + DA+ + I +N++ ++ GA AR Sbjct: 125 ARLLNMIAIGAYAELTGAVSLDALKAALTDALP---ERNHRFIPLNVQAIDLGAARAR 179 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: 231 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: 186 Length adjustment: 26 Effective length of query: 452 Effective length of database: 160 Effective search space: 72320 Effective search space used: 72320 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