Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_086508848.1 BZY95_RS04860 amidase
Query= SwissProt::Q38M35 (462 letters) >NCBI__GCF_002151265.1:WP_086508848.1 Length = 467 Score = 470 bits (1209), Expect = e-137 Identities = 240/457 (52%), Positives = 302/457 (66%), Gaps = 2/457 (0%) Query: 8 LAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQD 67 L + AA LR L+A L + +A NAY TW G A + A A D L+ QG D Sbjct: 11 LRQQAAALRNGTLSASELAEAACAAYASRGKHDNAYLTWQGEAALAFARATDALIAQGGD 70 Query: 68 LGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTVEF 127 GPLMG+PVS+KD+Y VPGLP +AGS LP +W+ GP+V L QL ++GKTHTVEF Sbjct: 71 SGPLMGIPVSIKDIYAVPGLPTYAGSSRRLPASWERPGPIVEALLAQLPSLMGKTHTVEF 130 Query: 128 AFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPASM 187 AFGGLG NAHWG PRNPW HR PGGSS+GAGVSL+ G+A LALGTDTAGSVR+PASM Sbjct: 131 AFGGLGTNAHWGAPRNPWDSQAHRTPGGSSSGAGVSLISGTAGLALGTDTAGSVRIPASM 190 Query: 188 TGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP--APV 245 TG GLKTT GRWP + IVPLS++LDT G+L R V+DLAYAF ALD P+P A Sbjct: 191 TGVAGLKTTAGRWPAQQIVPLSTTLDTPGLLARRVDDLAYAFDALDANLSPRPSPVSATP 250 Query: 246 RVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGGL 305 + L GVP + FWDD P IA AV+ A+++L AGA+VV LP+ +EA+++F++GGL Sbjct: 251 ELADLTFGVPESFFWDDCSPGIAEAVQQAIRQLEAAGARVVTLELPNTDEAYELFQKGGL 310 Query: 306 AASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDDV 365 AA+ELAA+L P + LDP V R+R A+ + + EY+RR+++L A V Sbjct: 311 AAAELAAFLKAELPEMEDALDPNVAARIRAADDMPAWEYVRRRSLLDELCTAATERMGQV 370 Query: 366 DVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVG 425 D +LTPTV +PP L + Y ANMKA+RNT ++N G C LT+PVG DA MPVG Sbjct: 371 DAVLTPTVAITPPTLESLEPEGAYPKANMKALRNTVMANFMGLCGLTLPVGRDAAGMPVG 430 Query: 426 LQLMGPPRAEARLIGIALGIEALIGQGHALLGAPDLP 462 LQ++ P EARL+ I IEA +G G +LG P P Sbjct: 431 LQVLAGPWQEARLLAIGQAIEAKLGTGPDILGEPSAP 467 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: 630 Number of extensions: 34 Number of successful extensions: 2 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: 467 Length adjustment: 33 Effective length of query: 429 Effective length of database: 434 Effective search space: 186186 Effective search space used: 186186 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