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 Ga0059261_0530 Ga0059261_0530 4-carboxy-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.1.1.-)
Query= SwissProt::Q9KWL3 (315 letters) >FitnessBrowser__Korea:Ga0059261_0530 Length = 315 Score = 522 bits (1345), Expect = e-153 Identities = 251/312 (80%), Positives = 280/312 (89%) Query: 1 MRIALAGAGAFGEKHLDGLKNIDGVEIVSIISRKAEQAAEVAAKYGAKHSGTDLSEALAR 60 M+IALAGAGAFGEKHLDGL+NIDGVE++S++ R+ E +VA KYG H+ T+L EAL + Sbjct: 1 MKIALAGAGAFGEKHLDGLRNIDGVEVISVVGRRLEPTQKVADKYGIPHATTELVEALEQ 60 Query: 61 DDVDAVILCTPTQMHAEQAIACMNAGKHVQVEIPLADSWADAEAVMKKSQETGLVCMVGH 120 +DAVILCTPTQMHA QAI CM+AGKHVQVEIPL DS AD EAV+ K+QETGL CMVGH Sbjct: 61 PGLDAVILCTPTQMHAAQAIQCMDAGKHVQVEIPLCDSLADGEAVLAKAQETGLTCMVGH 120 Query: 121 TRRFNPSHQYIHNKIVAGELAIQQMDVQTYFFRRKNMNAKGEPRSWTDHLLWHHAAHTVD 180 TRRFNPSHQY+H +I+AGELA+QQMDVQTYFFRRKNMNAKGE RSWTDHLLWHHAAHTVD Sbjct: 121 TRRFNPSHQYLHRRIMAGELAVQQMDVQTYFFRRKNMNAKGEARSWTDHLLWHHAAHTVD 180 Query: 181 LFAYQAGKIVQANAVQGPIHPELGIAMDMSIQLKSETGAICTLSLSFNNDGPLGTFFRYI 240 LFAYQAG IV ANA++GP HPELGIAMDMS+QLK+E+GAICTLSLSFNNDGPLGTFFRYI Sbjct: 181 LFAYQAGPIVAANAIEGPHHPELGIAMDMSLQLKAESGAICTLSLSFNNDGPLGTFFRYI 240 Query: 241 CDNGTWIARYDDLVTGKEEPVDVSKVDVSMNGIELQDREFIAAIREGREPNSSVARVLDC 300 CDNGTWIARYDDLVTGKEEPVD++ V V+ NGIELQDREFIAAIREGREPN+SVA+VL C Sbjct: 241 CDNGTWIARYDDLVTGKEEPVDLTGVTVTSNGIELQDREFIAAIREGREPNASVAQVLPC 300 Query: 301 YRVLGELEVQLE 312 YRVL LE QLE Sbjct: 301 YRVLDALEKQLE 312 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: 406 Number of extensions: 5 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: 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