Align 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase; CHMS dehydrogenase; 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase; EC 1.1.1.312 (characterized)
to candidate AZOBR_RS26915 AZOBR_RS26915 oxidoreductase
Query= SwissProt::Q9KWL3 (315 letters) >FitnessBrowser__azobra:AZOBR_RS26915 Length = 315 Score = 409 bits (1051), Expect = e-119 Identities = 204/313 (65%), Positives = 242/313 (77%), Gaps = 2/313 (0%) Query: 1 MRIALAGA-GAFGEKHLDGLKNIDGVEIVSIISRKAEQAAEVAAKYGAKHSGTDLSEALA 59 MRI +AGA GAFG KHL+ + IDGVE+VS++ + + A G H DL+E+L Sbjct: 1 MRICVAGAAGAFGVKHLEAVAAIDGVEVVSVVGGEPDDIEGFAKARGIPHWTKDLAESLE 60 Query: 60 RDDVDAVILCTPTQMHAEQAIACMNAGKHVQVEIPLADSWADAEAVMKKSQETGLVCMVG 119 R DV+AVIL TPT +HA QAI C+ AGKHV VEIP+ADS ADAE ++ + +GLV M G Sbjct: 61 RADVEAVILATPTPVHATQAIQCLEAGKHVLVEIPMADSLADAERLVAAQRTSGLVAMAG 120 Query: 120 HTRRFNPSHQYIHNKIVAGELAIQQMDVQTYFFRRKNMNAKGEPRSWTDHLLWHHAAHTV 179 HTRRFNPSHQ+I N++ AGEL IQQMDVQTYFFRR NMNA G+PR+WTDHLLWHHA HTV Sbjct: 121 HTRRFNPSHQWIRNRVQAGELTIQQMDVQTYFFRRSNMNALGKPRTWTDHLLWHHACHTV 180 Query: 180 DLFAYQAGKIV-QANAVQGPIHPELGIAMDMSIQLKSETGAICTLSLSFNNDGPLGTFFR 238 DLF YQ G++ Q +A+QGP HP+LGIAMDMSI +K +GAICTLSLSFNNDGPLGTFFR Sbjct: 181 DLFQYQTGEVASQMHALQGPAHPQLGIAMDMSIGMKVPSGAICTLSLSFNNDGPLGTFFR 240 Query: 239 YICDNGTWIARYDDLVTGKEEPVDVSKVDVSMNGIELQDREFIAAIREGREPNSSVARVL 298 YICDNGT+IARYDDL GK+ +D+S + VS NGIEL DREF AAIR+GREPN+SVA+ L Sbjct: 241 YICDNGTYIARYDDLYDGKDNKIDLSGLTVSTNGIELIDREFFAAIRDGREPNASVAQCL 300 Query: 299 DCYRVLGELEVQL 311 R L LE L Sbjct: 301 PAMRTLDRLEKSL 313 Lambda K H 0.319 0.133 0.394 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: 365 Number of extensions: 11 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: 315 Length of database: 315 Length adjustment: 27 Effective length of query: 288 Effective length of database: 288 Effective search space: 82944 Effective search space used: 82944 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