Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate YP_001327118.1 Smed_1437 short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000017145.1:YP_001327118.1 Length = 250 Score = 118 bits (296), Expect = 1e-31 Identities = 88/252 (34%), Positives = 132/252 (52%), Gaps = 15/252 (5%) Query: 6 KHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELG-DNARFAVADISDEQ 64 K +++G ASG+G A +L G KV L D NA A+ + D A+ ++DE+ Sbjct: 4 KSVLITGGASGIGFEIATLLNRRGWKVYLADRNAGALADACSVISLDPAQALACSVTDEE 63 Query: 65 AAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRL 124 +SA+ AA S+ L ++N AGI + + F ++++VNL G+F + R Sbjct: 64 QVRSAIKAAASS-APLGAIINSAGIAMDRPAVDTS----VDDFRRILDVNLTGTFIVCRE 118 Query: 125 AAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGI 184 AA AA G I+N +S++ G G+AAY ASKGA+ LT A EL + GI Sbjct: 119 AARHWLAIAAP-----GAIVNISSVSGLVGNKGRAAYGASKGAVNLLTYILATELGQDGI 173 Query: 185 RVMTIAPGIFETPMMAGM-SDEVRASLAAGVPFPPRLGRPQEYAALARHII--ENSMLNG 241 RV IAPG +TP+ + +++VRA +P R G +E A A +I E S +NG Sbjct: 174 RVNAIAPGAIDTPLSRAVHTEDVRAQWHERIP-QRRYGTSREVAQSAAFLISEEASYING 232 Query: 242 EVIRLDGALRMA 253 +V+ +DG A Sbjct: 233 QVLAVDGGFAHA 244 Lambda K H 0.318 0.131 0.358 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: 111 Number of extensions: 6 Number of successful extensions: 3 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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: 46 (22.3 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