Align 4-oxalocrotonate decarboxylase; 4-OD; EC 4.1.1.77 (uncharacterized)
to candidate WP_102999320.1 C1M55_RS04075 2-keto-4-pentenoate hydratase
Query= curated2:P49156 (264 letters) >NCBI__GCF_002893965.1:WP_102999320.1 Length = 261 Score = 181 bits (458), Expect = 2e-50 Identities = 99/251 (39%), Positives = 145/251 (57%) Query: 13 LAEHIENAELDVHDIPKVTNDYPDMTFADAYDVQWEIRRRKEARGNKVVGLKMGLTSWAK 72 LA+H+++AE D I + YPD+ DAY++Q RR+ A G KVVG K+GL+S A Sbjct: 10 LADHLDSAERDRAPISPLIATYPDIDVVDAYEIQLINIRRRVAGGAKVVGHKVGLSSLAM 69 Query: 73 MAQMGVETPIYGFLVDYFSVPDGGVVDTSKLIHPKIEAEISFVTKAPLHGPGCHIGQVLA 132 MGV+ P YG L+ + VDTS+ P++E E++F+ A L G GC V+ Sbjct: 70 QQMMGVDEPDYGHLLAEMEEFENRPVDTSRFCFPRVEVEVAFILGADLPGAGCTEQDVID 129 Query: 133 ATDFVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANVADLDLRTLGVVMEKN 192 AT P++E+IDSR +++K L +ADNASS FI G + +D+D++ + V+ N Sbjct: 130 ATVAYAPSIELIDSRIKDWKIGLSDTIADNASSAGFILGKERVRPSDIDIKAIDAVLTCN 189 Query: 193 GEVVELGAGAAVLGHPASSVAMLANLLAERGEHIPAGSFIMTGGITAAVPVAPGDNITVR 252 GE + G AVLG+P ++VA LA + G + AG ++ G T A+ PGDN Sbjct: 190 GERIAEGRSDAVLGNPVTAVAWLAQKVDTFGVWLKAGDIVLPGSCTRAIDAHPGDNFRAE 249 Query: 253 YQGLCSVSARF 263 + GL SVS +F Sbjct: 250 FSGLGSVSLQF 260 Lambda K H 0.320 0.136 0.396 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: 195 Number of extensions: 9 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: 264 Length of database: 261 Length adjustment: 25 Effective length of query: 239 Effective length of database: 236 Effective search space: 56404 Effective search space used: 56404 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 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