Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate SMc02881 SMc02881 hypothetical protein
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Smeli:SMc02881 Length = 453 Score = 246 bits (628), Expect = 1e-69 Identities = 164/453 (36%), Positives = 242/453 (53%), Gaps = 19/453 (4%) Query: 7 SLAEHAARLRRRELTAVALIDTCAQHHARME--PRLNAYKTWDGARARSAAAAVDTLLDQ 64 +LA A ++ +L VAL+ A+ R+E P + + RA A A + Sbjct: 6 TLASLAVLVQSGKLDPVALV---AETLTRIEDHPDRSIFVALTQERAAREAKAASARIKT 62 Query: 65 GQDLGPLMGLPVSVKDLYGVPGLPVFAGS---DEALPEAWQAAGPLVARLQRQLGIVVGK 121 G+ LG L GLPV+ KDL+ + G AGS E P A A ++A L + +G+ Sbjct: 63 GRSLGLLDGLPVAWKDLFDLAGSITTAGSVVLAEGSPAAADAT--VIADLGSAGMVSIGR 120 Query: 122 THTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSV 181 T+ EFAF GLG+N H+GTPRNP S HR+PGGSS+G+ ++ G LA+GTDT GSV Sbjct: 121 TNMSEFAFSGLGINPHYGTPRNPRSADVHRIPGGSSSGSAAAVAAGLVPLAIGTDTGGSV 180 Query: 182 RVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPA 241 R+PA+MTG VG K T GR+ ++G+ PL+ SLD+ G L +TV+D +A AA+ GL A Sbjct: 181 RIPAAMTGIVGYKATRGRYAMKGVFPLAQSLDSLGPLCQTVQDAVWADAAM----HGLTA 236 Query: 242 PAPVR--VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDI 299 P R + L + VP +DD + + AA E A++RL AGA+V R P E F++ Sbjct: 237 PVIRRAEIADLSIVVPETIVFDDAEAEVVAAFEEAIKRLEAAGAKVRRQAFPSFAEIFEL 296 Query: 300 FRRGG--LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAG 357 R G + A A + ++ + ER+DP V R R E+++ +Y+ R Sbjct: 297 TARHGALVTAEAYALHRERLAGPEAERMDPRVVARTRLGEKITVSDYIALLDARDRLIHE 356 Query: 358 AARLFDDVDVLLTPTVP-ASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVG 416 +++ PT+P +PP + + + N + +RNT+I N +C +++P G Sbjct: 357 TIETLKAGELIAHPTLPHVAPPLDPLLADDDLFFKVNARTLRNTSIGNFLDFCGVSIPCG 416 Query: 417 LDANRMPVGLQLMGPPRAEARLIGIALGIEALI 449 A MP G QL P + RL+ AL EA I Sbjct: 417 TGAAGMPAGFQLAAPHHQDDRLLSAALAAEASI 449 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: 457 Number of extensions: 29 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: 453 Length adjustment: 33 Effective length of query: 429 Effective length of database: 420 Effective search space: 180180 Effective search space used: 180180 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