Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_011384077.1 AMB_RS08440 amidase
Query= SwissProt::Q38M35 (462 letters) >NCBI__GCF_000009985.1:WP_011384077.1 Length = 391 Score = 147 bits (371), Expect = 6e-40 Identities = 117/384 (30%), Positives = 182/384 (47%), Gaps = 22/384 (5%) Query: 65 GQDLGPLMGLPVSVKDLYGVPGLPVFAGSDE--ALPEAWQAAGPLVARLQRQLGIVVGKT 122 G + GPL GL + KD++ V G AG+ + L E + + L +VGKT Sbjct: 18 GAETGPLAGLTFAAKDVFDVAGYVTGAGNPDWRRLAEPAKHTAWAIGTLLESGARLVGKT 77 Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182 HT E G G N+H+GTP NP +P VPGGSS+G+ ++ G +ALGTDTAGS R Sbjct: 78 HTDELTRGIFGDNSHYGTPDNPRAPGH--VPGGSSSGSAAAVAGGLCSMALGTDTAGSTR 135 Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP 242 VPAS G GL+ T+G P++G++ S++ DT G+L E LA AL + P Sbjct: 136 VPASFCGVFGLRPTLGTIPMDGVLSQSNTFDTVGLLADDPEILAKMGEALLRKKIKDTRP 195 Query: 243 APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVR----FPLPHCEEAFD 298 A V V + DP++AAA+EAA+ R+ +A A +VR P+P + Sbjct: 196 AQV--------VVLEDALEASDPAVAAAIEAALPRIKEAVAPIVRGRKLSPVPLADW--- 244 Query: 299 IFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGA 358 + + + E + + R V D +VS + R Sbjct: 245 VEHQNAIQGREAWETFGEWINNSNPRFGFEVADNFLRGSKVSQRTLSAARGFRLRAKRWV 304 Query: 359 ARLFDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLD 418 + +L+ PT P + P + +V + ++ T I+ + G +++P+ Sbjct: 305 QEALEGNAMLVLPTTPVTAPPVHSPRSVMWEIRHRIVSL--TTIAGMAGCPQISLPL-CK 361 Query: 419 ANRMPVGLQLMGPPRAEARLIGIA 442 + +PVGL L+GP ++A L+ A Sbjct: 362 VDGLPVGLSLIGPRGSDALLLAAA 385 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: 442 Number of extensions: 23 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: 462 Length of database: 391 Length adjustment: 32 Effective length of query: 430 Effective length of database: 359 Effective search space: 154370 Effective search space used: 154370 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 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