Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_015446808.1 R2APBS1_RS02860 amidase
Query= SwissProt::Q38M35 (462 letters) >NCBI__GCF_000230695.2:WP_015446808.1 Length = 465 Score = 149 bits (377), Expect = 1e-40 Identities = 133/435 (30%), Positives = 195/435 (44%), Gaps = 35/435 (8%) Query: 24 ALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYG 83 AL D Q R++P+L+AY + AA + G +G L G+P+++KD + Sbjct: 33 ALADVYQQAIERIDPQLHAYVDQRSGLVQDQAALAERRRRDGV-IGRLDGIPIALKDNFD 91 Query: 84 VPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRN 143 + G P G + A +VARL+ +++GKT+ E A G + N H G N Sbjct: 92 IAGWPTRVGLPGRGKPVREDAH-VVARLRASGAVLLGKTNMDEGALGAVTDNPHSGATHN 150 Query: 144 PWSPHEHR-VPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPV 202 P H H GGSS GA ++ G A+ A+G+D+ GS+R+PAS G LK T G Sbjct: 151 P---HRHGYTAGGSSGGAAAAVAAGLAVAAVGSDSLGSIRIPASYCGVYALKPTHGEISA 207 Query: 203 EGIVPLSSSLDTAGVLTRTVEDLAYAFAAL------DTESQ------GLPAPAPVRVQGL 250 G+VP + LD G+L R+ +DL L D S+ LP P L Sbjct: 208 RGLVPAARRLDAVGLLARSADDLTVLLQVLAGYDADDARSRRRRVAFALPDWEP---GNL 264 Query: 251 RVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGGLAASEL 310 R G+ + + P + EAA+ +L A R + + F RR GL E Sbjct: 265 RAGLLPDLAAVGVQPEVIEVFEAAMAKLPHALGD--RRTVDFADWDFARTRRAGLLLME- 321 Query: 311 AAYLDQHFPHKVERLDPV---VRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDDVDV 367 A L + PV R + +A S+ +Y VL RLF VDV Sbjct: 322 AEMLGTFAADLADSRRPVSERFRRLLGYAAGKSAADYAVADRVLDAATLKMRRLFAQVDV 381 Query: 368 LLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQ 427 L+ PT P G P T+ ++L G A+++P+G+ N MPVGLQ Sbjct: 382 LVLPTTPQ--------GAFPLDGPVPDSQADLTSFASLAGCPAVSLPMGMLPNGMPVGLQ 433 Query: 428 LMGPPRAEARLIGIA 442 L+G ++ RL+ +A Sbjct: 434 LVGARGSDLRLLELA 448 Lambda K H 0.320 0.135 0.411 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: 501 Number of extensions: 32 Number of successful extensions: 6 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: 462 Length of database: 465 Length adjustment: 33 Effective length of query: 429 Effective length of database: 432 Effective search space: 185328 Effective search space used: 185328 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: 51 (24.3 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