Align 2-keto-4-pentenoate hydratase; 2-hydroxypentadienoic acid hydratase; EC 4.2.1.80 (characterized)
to candidate WP_011383245.1 AMB_RS04100 2-oxo-hepta-3-ene-1,7-dioic acid hydratase
Query= SwissProt::Q9S156 (260 letters) >NCBI__GCF_000009985.1:WP_011383245.1 Length = 268 Score = 168 bits (426), Expect = 9e-47 Identities = 98/264 (37%), Positives = 144/264 (54%), Gaps = 8/264 (3%) Query: 3 TTTQIQAWAERLRHAEATATPIAPLREEITDND--SAYAVQLVNVQYAQSQGRRIVGRKI 60 T QI A A RL AE T + + + AYAVQ V+ ++GR++VG KI Sbjct: 4 TLDQINAAAARLHRAEQTRHQCGQISLDHPEMGMADAYAVQKAWVETKINEGRKVVGHKI 63 Query: 61 GLTSLAVQKQLGVDQPDFGTLFADMLYGDDEAVPLSRTLQPKVEAEVALVLAKDLERPDT 120 GLTS A+Q+ +D+PD+GTL DM++G+ +P++R + P VE E+A +L LE PD Sbjct: 64 GLTSRAMQQSSQIDEPDYGTLLDDMVFGEGTDIPMARFIVPMVEVELAFILKDRLEGPDV 123 Query: 121 TLVDVISATAYVLPAIEIVGSRIADWN------IRFIDTVADNASSGLVVLGAVPTALNA 174 TL V+SAT YV+PA+EI+ +R + + DT++DNA++ +V+G P Sbjct: 124 TLTQVLSATDYVIPALEIIDARCHRLDPETKRPRKVFDTISDNAANAGIVMGGRPVRPMD 183 Query: 175 LDLKLCQMQMTRNGDVVSTGSGGACLGHPLNAAVWLARRLANLGQPLRAGDLVLTGALGP 234 +DL+ M RNG + TG L HP + WLAR+ A L G +VL G+ Sbjct: 184 VDLRWVAAIMYRNGVIEETGVAAGVLNHPAHGISWLARKFAPHSIALEPGQVVLAGSFTR 243 Query: 235 MVAVNAGDRFEARISGIGSVCAQF 258 V AGD F +G++ +F Sbjct: 244 PVPARAGDTFHVDYGPLGAIACRF 267 Lambda K H 0.319 0.134 0.386 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: 173 Number of extensions: 9 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: 260 Length of database: 268 Length adjustment: 25 Effective length of query: 235 Effective length of database: 243 Effective search space: 57105 Effective search space used: 57105 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 (21.7 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