Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate RR42_RS07975 RR42_RS07975 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Cup4G11:RR42_RS07975 Length = 444 Score = 244 bits (624), Expect = 3e-69 Identities = 164/447 (36%), Positives = 240/447 (53%), Gaps = 14/447 (3%) Query: 7 SLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTW----DGARARSAAAAVDTLL 62 ++A AA L T+VAL + Q AR++ NA T DGA A +AA A D Sbjct: 7 TIAALAADLAAGRTTSVALTE---QALARIDGHRNAGGTAFLEVDGAGALAAARAADQAR 63 Query: 63 DQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKT 122 G PL GLPVS+KDL+ V G AGS E A P+VARL+ +++G+T Sbjct: 64 AAGLVASPLAGLPVSIKDLFDVKGQVTRAGSKALAGEPASADAPVVARLRAAGAVLIGRT 123 Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182 + EFAF GLG+N H+GTPR P+ + R+ GGS++G +S+ A+ ALGTDT GS+R Sbjct: 124 NMSEFAFSGLGLNPHYGTPRTPFD--DARIAGGSTSGGALSVALDLAVAALGTDTGGSIR 181 Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP 242 +P++ G G K T R P+ G VPLS+SLD+AG L R+V A AF A+ + P Sbjct: 182 IPSAFCGLTGFKPTASRVPLAGAVPLSTSLDSAGPLARSVACCA-AFDAIVSGETLDSRP 240 Query: 243 APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRR 302 AP + GLR+ V + D +D +A A + + L++ GAQ++ F P + I Sbjct: 241 AP--LGGLRLLVTRDFVCDGLDAEVAQAFDVTLATLSRLGAQIIPFDFPELKRLPQINAA 298 Query: 303 GGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLF 362 GGL A+E + + + DP V R+R EQ+ + +Y+ A + A AA L Sbjct: 299 GGLTAAEAWHWHKPLLAERGDAYDPRVAMRIRRGEQLGAADYIELLAERRAMQARAAGLL 358 Query: 363 DDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRM 422 + D L PTV PPRL + + E + N +RN ++ N CA+++P + A Sbjct: 359 READAWLMPTVAVRPPRLDALQSDEAFFATNGLVLRNPSVLNFLDGCAVSLP--MPAAEQ 416 Query: 423 PVGLQLMGPPRAEARLIGIALGIEALI 449 +GL + G +AR++ +A IEA + Sbjct: 417 GMGLSVGGLNGRDARVLQVAGAIEAAL 443 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: 488 Number of extensions: 24 Number of successful extensions: 3 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: 444 Length adjustment: 33 Effective length of query: 429 Effective length of database: 411 Effective search space: 176319 Effective search space used: 176319 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