Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF63 HP15_63 2-oxoisovalerate dehydrogenase, E1 component, beta subunit
Query= reanno::Smeli:SMc03202 (337 letters) >FitnessBrowser__Marino:GFF63 Length = 268 Score = 407 bits (1046), Expect = e-118 Identities = 183/266 (68%), Positives = 220/266 (82%) Query: 70 MAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGGIFGGQTH 129 M AYGL+P EIQFADY+ PAYDQL EAAR+RYRS G+F PI VR P GGGIFGGQTH Sbjct: 1 MGAYGLRPVAEIQFADYILPAYDQLVSEAARLRYRSGGEFWAPITVRSPYGGGIFGGQTH 60 Query: 130 SQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFDGHHERPV 189 SQSPEA+F H+ GLK V+PSNPYDAKGLLIS+IE DP++FLEPKR+YNGPFDGHHER + Sbjct: 61 SQSPEAIFAHITGLKTVIPSNPYDAKGLLISSIESDDPIIFLEPKRIYNGPFDGHHERQI 120 Query: 190 TAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGIDAEVIDL 249 +W+ H VP+GHYT+P+GKA R GS VTV+AYG MVHVA A EE+G+DAE++DL Sbjct: 121 KSWADHPDASVPEGHYTVPLGKAATVRHGSDVTVLAYGAMVHVAKAGIEESGVDAELLDL 180 Query: 250 RSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPVVRLTGWD 309 RS++PLD++ IVQS KKTGRCV++HEA+ GFG EL+ALVQE CFYHL+SP+ R+ GWD Sbjct: 181 RSIVPLDIDAIVQSVKKTGRCVILHEASRYGGFGGELSALVQERCFYHLKSPIERVAGWD 240 Query: 310 TPYPHAQEWDYFPGPARVGRALAEAM 335 TPYPHA EWDYFPGP R+ +AL ++M Sbjct: 241 TPYPHAFEWDYFPGPMRLAKALQKSM 266 Lambda K H 0.321 0.138 0.424 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: 385 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: 337 Length of database: 268 Length adjustment: 27 Effective length of query: 310 Effective length of database: 241 Effective search space: 74710 Effective search space used: 74710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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