Align protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8) (characterized)
to candidate Ac3H11_1163 Protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8)
Query= metacyc::MONOMER-15117 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1163 Length = 281 Score = 257 bits (657), Expect = 2e-73 Identities = 126/282 (44%), Positives = 182/282 (64%), Gaps = 6/282 (2%) Query: 1 MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60 MA++ G+ +SHIPA+G AI G ++ YW P F G+ PIR W+ + PDVV++ YND Sbjct: 1 MAQLIGGLGTSHIPAIGNAIHKGLQNDPYWKPFFDGFPPIRQWLGE--KKPDVVVMFYND 58 Query: 61 HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120 H F ++ +PTFA+G A + ADEGWG +P G DL+WH+ +L+ EFD+T Sbjct: 59 HGLNFFLDKMPTFAVGAAAQYNNADEGWGIPTLPPFPGEVDLSWHLINTLVEQEFDVTTC 118 Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFP 180 +M VDH CT+PL + + E + P V+P +N V +P PS KRC+ALG ++ A++S+ Sbjct: 119 QEMLVDHACTLPLKLFWPEGD-CPVTVVPVCINTVQFPLPSAKRCYALGKAVGQAIQSWD 177 Query: 181 EDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEG 240 D V V +GG+SHQL G RAG INK FDL FI+ L ++PE ++ + + ++G++G Sbjct: 178 SDKKVAVIASGGLSHQLDGERAGFINKAFDLQFIESLTTNPEWATQFSVHKLVEKTGTQG 237 Query: 241 VELVMWLIMRGALPEK---VRDLYTFYHIPASNTALGAMILQ 279 VEL+MW+ MRGAL VR +++ YHIP SNTA M L+ Sbjct: 238 VELLMWVAMRGALATASAGVRRVHSNYHIPISNTATAVMALE 279 Lambda K H 0.319 0.138 0.439 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: 297 Number of extensions: 16 Number of successful extensions: 4 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: 302 Length of database: 281 Length adjustment: 26 Effective length of query: 276 Effective length of database: 255 Effective search space: 70380 Effective search space used: 70380 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