Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate CCNA_00092 CCNA_00092 short chain dehydrogenase
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Caulo:CCNA_00092 Length = 296 Score = 145 bits (365), Expect = 1e-39 Identities = 105/265 (39%), Positives = 141/265 (53%), Gaps = 32/265 (12%) Query: 1 MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKLD----- 55 M RL GK A+IT GIGL T ELF EGA V+A D++ + G+ +E R D Sbjct: 1 MVGRLNGKVAVITGGCSGIGLGTVELFVAEGACVVAADLQDE--KGRMLEQRFPDQVRFA 58 Query: 56 ----VRDDAAIKALA---AEIGAVDVLFNCAGFVHAG---NILECSEEDWDFAFDLNVKA 105 DD K +A + G +D+LFN AG H G ++ E + E WD F L V+ Sbjct: 59 RCDVTADDDLAKTMALAESSFGGLDILFNNAG--HGGTPASVPELTAEAWDKTFALLVRG 116 Query: 106 MYRMIRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITR 165 + LP M +GGGSIIN +S A G AYS++KAAVI +++ AA+ + Sbjct: 117 PAMGMTHALPLMQKRGGGSIINTASIAGLQAGF-GPLAYSSAKAAVIHMSRCAAAELSPQ 175 Query: 166 GVRCNAICPGTVA------SPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEI 219 +R NAICPG +A S L + + Q AQ A++ QP+ + G PE+I Sbjct: 176 KIRVNAICPGLIATSIFGASMGLPREVADQMAAQIASIGP------KIQPIPKSGLPEDI 229 Query: 220 AALALYLGSDESSFTTGHAHVIDGG 244 AA ALYL SD+S F TG V+DGG Sbjct: 230 AAAALYLASDDSRFVTGTHIVVDGG 254 Lambda K H 0.320 0.133 0.381 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: 186 Number of extensions: 6 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: 247 Length of database: 296 Length adjustment: 25 Effective length of query: 222 Effective length of database: 271 Effective search space: 60162 Effective search space used: 60162 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: 47 (22.7 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