Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_013646016.1 METBO_RS12145 ketoisovalerate oxidoreductase subunit vorA
Query= SwissProt::P80907 (478 letters) >NCBI__GCF_000191585.1:WP_013646016.1 Length = 481 Score = 697 bits (1798), Expect = 0.0 Identities = 337/471 (71%), Positives = 398/471 (84%), Gaps = 1/471 (0%) Query: 3 KKVIRKPDSLHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVG 62 +K++ KP+++ F RKGGSAPTATHYC+GCGHGILHKLIGEA+D+L IQ+R VM SPVG Sbjct: 8 EKILGKPETILSEFPRKGGSAPTATHYCSGCGHGILHKLIGEAVDDLKIQDRMVMTSPVG 67 Query: 63 CAVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANR 122 CAVFAYYYFDCG+VQVAHGRAPAVGTG+SRAE+ VV+LYQGDGDLASIGLNETIQAANR Sbjct: 68 CAVFAYYYFDCGHVQVAHGRAPAVGTGLSRAEEDAVVILYQGDGDLASIGLNETIQAANR 127 Query: 123 GEKMAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPV 182 GEKMAVFF+NNTVYGMTGGQMAPTTLIGEVTVTC GRDPRY GYPLHM ELL+NL+APV Sbjct: 128 GEKMAVFFINNTVYGMTGGQMAPTTLIGEVTVTCQDGRDPRYTGYPLHMSELLNNLKAPV 187 Query: 183 FIERVSLADPKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEE 242 FIERVSL+DP IRKA+RAV++ALEIQRDGKGYAFVE+LSPCPTNLRQDAEGAE+FL E+ Sbjct: 188 FIERVSLSDPSHIRKARRAVRKALEIQRDGKGYAFVELLSPCPTNLRQDAEGAEKFLNEQ 247 Query: 243 MEREFPVKNFRDRSSETEPLIRSESDFSRESLDRIFQIKEDSVPDPVDDPEFREVRVKIA 302 ME EFP+ NFRDR++E EPL R SDFSRESLD+IF + E+S +DDPEF VKI+ Sbjct: 248 MEVEFPLANFRDRTAEVEPLCRESSDFSRESLDKIFDVGEESSLGAIDDPEFETKVVKIS 307 Query: 303 GFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDTPD 362 GFGGQGVLSMGL LA+AAC RH SWYP+YGPEQRGGTS+C V++SGE +GSP V D Sbjct: 308 GFGGQGVLSMGLILAEAACKARRHVSWYPSYGPEQRGGTSNCTVIVSGEIIGSPVVYRSD 367 Query: 363 VLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKENLRAIGVPALEIAKEHGTGRAANT 422 +LVA N+PSL+EFA V++GG +LYD DF E ++AIGVPAL+IAKE+G G+AANT Sbjct: 368 ILVALNRPSLEEFAERVKQGGTILYDEEIGDFKPPEGVKAIGVPALKIAKENGVGKAANT 427 Query: 423 AMLGVMMALGITGLDEESFRDAIRFTFSGKDKIIDINLKILEAGADWARKN 473 AMLGV+M + + + F+ AI TF+ K +ID+NL++L A A+WAR+N Sbjct: 428 AMLGVLMEVS-DDMSVDDFKSAISQTFAKKPHLIDLNLEVLYAAAEWAREN 477 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: 774 Number of extensions: 31 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: 481 Length adjustment: 34 Effective length of query: 444 Effective length of database: 447 Effective search space: 198468 Effective search space used: 198468 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: 51 (24.3 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