Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate CA265_RS18405 CA265_RS18405 dehydrogenase
Query= reanno::Smeli:SMc03202 (337 letters) >FitnessBrowser__Pedo557:CA265_RS18405 Length = 658 Score = 249 bits (636), Expect = 1e-70 Identities = 139/310 (44%), Positives = 192/310 (61%), Gaps = 23/310 (7%) Query: 7 IEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESGIVGT 66 ++A+ +D++M + N+V+ G+D+ +GG F+ T G AKYG+ R +TPI ES IVG Sbjct: 344 LDAITDGLDLAMQKYPNLVLMGQDIADYGGAFKITDGFTAKYGRGRVRNTPICESAIVGA 403 Query: 67 AIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGGIFGG 126 +G++ G K VE+QFAD++ ++Q+ A+ YR +VVRMPTG G G Sbjct: 404 GLGLSINGYKAVVEMQFADFVTVGFNQIVNNLAKTHYRWGE--KADVVVRMPTGAGTGAG 461 Query: 127 QTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFDGHHE 186 HSQS EA FT GLK+V P+ P DAKGLL++AIEDP+PV++ E K LY Sbjct: 462 PFHSQSNEAWFTKTPGLKIVYPAFPEDAKGLLLAAIEDPNPVLYFEHKYLY--------- 512 Query: 187 RPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAE---ETGID 243 R ++A VPDG+YT IGKA +G T+I YG VH AL E E+G Sbjct: 513 RSLSA-------PVPDGYYTTEIGKAVRLAEGDKFTIITYGLGVHWALDYMEQYPESG-- 563 Query: 244 AEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPVV 303 A +IDLR+L P D ET+ + K TGR +++HE TLT+GFGAEL+A + EHCF +L++PV+ Sbjct: 564 ATLIDLRTLQPWDKETVSAAVKATGRVLILHEDTLTNGFGAELSAWIGEHCFAYLDAPVM 623 Query: 304 RLTGWDTPYP 313 R DT P Sbjct: 624 RCASLDTAIP 633 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: 577 Number of extensions: 29 Number of successful extensions: 4 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: 658 Length adjustment: 33 Effective length of query: 304 Effective length of database: 625 Effective search space: 190000 Effective search space used: 190000 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: 51 (24.3 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