Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 208875 DVU3348 pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit, putative
Query= SwissProt::P80907 (478 letters) >MicrobesOnline__882:208875 Length = 260 Score = 251 bits (640), Expect = 3e-71 Identities = 118/229 (51%), Positives = 156/229 (68%) Query: 26 ATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCGNVQVAHGRAPA 85 ATHYC GC HG+ H+L+ E + E+G+ E ++ +S +GC+VF Y Y V+ HGRAPA Sbjct: 24 ATHYCPGCHHGVAHRLVAEVLTEMGVAEDTICVSSIGCSVFIYNYLAVDTVEAPHGRAPA 83 Query: 86 VGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNTVYGMTGGQMAP 145 V TG+ RA +V YQGDGDLASIGL E + AANRGE+M + FVNNTVYGMTGGQMAP Sbjct: 84 VATGVKRARKDKIVFAYQGDGDLASIGLAEIMHAANRGERMTIVFVNNTVYGMTGGQMAP 143 Query: 146 TTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKSIRKAKRAVKRA 205 TTL+G+ T TCP GR G P+ M E++ L + RVSL K IR AK+A+++A Sbjct: 144 TTLVGQKTTTCPSGRCRDTEGLPMKMAEIIAGLGGVAYSARVSLDSVKHIRAAKKALRKA 203 Query: 206 LEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFRD 254 ++Q++ G+ FVE+LS CPTN R DA A + + EEM FP+ ++D Sbjct: 204 FDVQQNDLGFGFVEMLSACPTNWRMDAVKANKRIAEEMIPYFPLGVYKD 252 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: 320 Number of extensions: 14 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: 260 Length adjustment: 29 Effective length of query: 449 Effective length of database: 231 Effective search space: 103719 Effective search space used: 103719 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 208874 DVU3347 pyruvate ferredoxin/flavodoxin oxidoreductase family protein
Query= SwissProt::P80907 (478 letters) >MicrobesOnline__882:208874 Length = 182 Score = 124 bits (312), Expect = 2e-33 Identities = 75/178 (42%), Positives = 104/178 (58%), Gaps = 7/178 (3%) Query: 299 VKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAV 358 V +AGFGGQGV+ +G LA A G + ++ P YGPE RGGT++C VV+S E +GSP + Sbjct: 7 VIMAGFGGQGVMLIGNLLAYAGMHAGLNVTYIPVYGPEMRGGTANCTVVVSDEDIGSPII 66 Query: 359 DTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKE-NLRAIGVPALEIAKEHGTG 417 P L+ NQPSLD+F + +GG+ + +T+ D SK E +R + VPA EIA G Sbjct: 67 QRPKSLIIMNQPSLDKFEARLEDGGVQVLNTSLVDASKAEARVRTVCVPANEIADGIGNT 126 Query: 418 RAANTAMLGV-MMALGITGLD--EESFRDAIRFTFSGKDKIIDINLKILEAGADWARK 472 + AN LG + A GI L+ +ES + I +S +I N L+AG D A K Sbjct: 127 KMANMVALGAYVQATGIVPLEAVKESLKSVISAHYS---HLIPKNADALQAGFDHAAK 181 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: 182 Number of extensions: 10 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: 182 Length adjustment: 26 Effective length of query: 452 Effective length of database: 156 Effective search space: 70512 Effective search space used: 70512 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 17 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