Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 (characterized)
to candidate PfGW456L13_2503 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.-)
Query= SwissProt::P23106 (281 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2503 Length = 275 Score = 115 bits (287), Expect = 1e-30 Identities = 89/278 (32%), Positives = 127/278 (45%), Gaps = 32/278 (11%) Query: 15 LAAGYRTNLHDQGEGFPALLIHGSGPASPPGPTGAGSFRSSQTR------RVIAPDMLGF 68 L G + + D G G P + IHGSGP G +G +F+ + RVI PD+ G+ Sbjct: 12 LPDGLQLHYKDTGNGEPVIFIHGSGP----GASGHSNFKQNYPLFTEAGYRVIVPDLPGY 67 Query: 69 GYSERPADGKYSQARWVEHAIGVLDALGIQQGDIVGNSFGGGLALALAIRHPERVRRLVL 128 G S++P D Y+ +V G+LDAL IQ+ +VGNS GG +A+ LA+ P+R+ RLVL Sbjct: 68 GASDKP-DTLYTLDFFVAALSGLLDALDIQRCVLVGNSLGGAIAIKLALDQPQRISRLVL 126 Query: 129 MGSVGVSFP----------ITAGLETAWGYTPSLANMRRLLDLFAHDRTLVNDELAELRY 178 M G+ G A G A MRRLL L D TL++DE R Sbjct: 127 MAPGGLMEKEQYYLQMEGIQKMGAAFAKGELNDAAGMRRLLALQLFDETLISDETVNERV 186 Query: 179 QASIRPGFQESFAAMFPPPRQNGVDDLASNETDIRALPNETLVIHGREDRIIPLQASLTL 238 A ++ Q+ + N L + I L G D+ P + T+ Sbjct: 187 -AVVK---QQPVCVLSTMQVPNMTSRLGELQCPI-------LGFWGMNDKFCPSSGAQTM 235 Query: 239 AQWIPNAQLHVFGQCGHWTQIEHAERFARLVENFLAEA 276 + + + +CGHW Q+EH + F R F EA Sbjct: 236 LEHCTQIRFVMLSECGHWVQVEHRDFFNRQCLAFFQEA 273 Lambda K H 0.320 0.137 0.416 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: 187 Number of extensions: 10 Number of successful extensions: 5 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: 281 Length of database: 275 Length adjustment: 25 Effective length of query: 256 Effective length of database: 250 Effective search space: 64000 Effective search space used: 64000 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