Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_086508811.1 BZY95_RS04655 amidase
Query= SwissProt::Q38M35 (462 letters) >NCBI__GCF_002151265.1:WP_086508811.1 Length = 468 Score = 137 bits (345), Expect = 8e-37 Identities = 130/460 (28%), Positives = 193/460 (41%), Gaps = 36/460 (7%) Query: 1 MNAAHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDT 60 M+A L + + E T AL + R +NAY D A +AA A + Sbjct: 9 MDAGQLRALFESGKASPLEATRAAL-----ERIERFNEAVNAYVLVDREGAETAAEASNK 63 Query: 61 LLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVG 120 QG+ L + G+PVS+KDL GLP GS + P L+ +++G Sbjct: 64 RWQQGRPLSAIDGIPVSLKDLTESVGLPARKGSLTVSDAPCERDSPPARMLREAGAVILG 123 Query: 121 KTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGS 180 KT+T EF + + N +G NPW PGGSS GA V+ +L G D+ GS Sbjct: 124 KTNTPEFGWKAITDNRVFGATANPWD--TRLTPGGSSGGAAVAAALNMGVLHQGGDSGGS 181 Query: 181 VRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTES---- 236 +R+PAS TG G K T G W E ++L G LTRTVED + Sbjct: 182 IRIPASFTGVFGFKPTFG-WVPEWPRSKEATLSHLGPLTRTVEDAVRMLNVMGRYDYRDP 240 Query: 237 ---QGLPA----PAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFP 289 +G PA ++G+R+ + ++P +A V A RL GA VV Sbjct: 241 YALRGQPADWGEELGQGIEGMRIAFSPTLGYARVEPEVAECVRQAAHRLEALGA-VVEEV 299 Query: 290 LPHCEEAFDIFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKA 349 P E IF AS LA Y +H + LD + + AE++S+++ Sbjct: 300 DPGFESPIRIFNTLWFTAS-LAVY-REHSERQRRLLDSGLVADAKRAERLSALDMFYALR 357 Query: 350 VLQRCGAGAARLFDDVDVLLTPTVPASP-------PRLADIGTVETYAPANMKAMRNTAI 402 R +++TP+V P P + + E +AP + Sbjct: 358 DRARLTESLEHFNQRYHLVMTPSVAVRPFPLHHDVPPGSGMRDWEEWAPFSYP------- 410 Query: 403 SNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 NL A ++P G + +PVG QL G +AR++ ++ Sbjct: 411 FNLSQQPAASIPCGFTPDGLPVGFQLAGGKHDDARVLRVS 450 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: 481 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: 468 Length adjustment: 33 Effective length of query: 429 Effective length of database: 435 Effective search space: 186615 Effective search space used: 186615 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