Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate CCNA_02696 CCNA_02696 AtzE family amidohydrolase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Caulo:CCNA_02696 Length = 464 Score = 166 bits (421), Expect = 1e-45 Identities = 150/479 (31%), Positives = 217/479 (45%), Gaps = 47/479 (9%) Query: 7 SLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQ 66 S+ E A +R +TA A+ + R++ +NA+ RA +AA AVD L G+ Sbjct: 5 SVVEIAGEVRAGRVTARAVTEATLSRIQRLDGGINAFTAVTAERALAAAEAVDADLAAGR 64 Query: 67 DLGPLMGLPVSVKDLYGVPGLPVFAGSD---EALPEAWQAAGPLVARLQRQLGIVVGKTH 123 +GPL G+P +VK+L+ + GLP AGS A P A A LV RL ++VG + Sbjct: 65 PVGPLAGVPFAVKNLFDLEGLPTLAGSKIRRAAAPPAHDAT--LVQRLTAAGAVLVGALN 122 Query: 124 TVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRV 183 EFA+G + NAH G RNP P R+ GGSS G+ ++ G L LG+DT GS+R+ Sbjct: 123 MDEFAYGFVTENAHDGPVRNPHDPT--RIAGGSSGGSAAAVAAGLVPLTLGSDTNGSIRI 180 Query: 184 PASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPA 243 PA + G GLK T GR +G+ P SLD G R+VEDLA A+ L P+ Sbjct: 181 PAGLCGVFGLKPTYGRLSRQGVFPFVESLDHVGPFARSVEDLALAYDVLQGPD---PSGD 237 Query: 244 PVRV---------------QGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRF 288 P+ + Q LRVGV F P + AA+ L ++ Sbjct: 238 PICIRDAEPLAGRLDALAEQPLRVGVLGGWFQQGAFPEVLAALGRVADALEARDEVTLQN 297 Query: 289 PLPHCEEAFDI--FRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSS--VEY 344 AF + F G L +LA + DP VRDR+ + + E Sbjct: 298 AQAARAAAFCLTAFEGGELHHEDLA--------RRAMDYDPAVRDRLLAGALLPAGVAEA 349 Query: 345 LRRKAVLQRCGAGAARLFDDVDVLLTP-TVPASPP---RLADIGTVETYAPANMKAMRNT 400 +R + R +F D+LL P +V +PP ++ V N+ A T Sbjct: 350 AQRFRTIFR--DEVREVFQRYDILLAPASVCPAPPIGQATMEMDGVPVSVRKNLGAF--T 405 Query: 401 AISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIE-ALIGQGHALLGA 458 + G L PV ++P+G+Q++ PP E AL ++ A + H +GA Sbjct: 406 QPISYVGLPVLAAPVN-RPGQLPIGVQIIAPPWREDLAFAAALRLQRAGVVAAHPPMGA 463 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: 517 Number of extensions: 28 Number of successful extensions: 4 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: 464 Length adjustment: 33 Effective length of query: 429 Effective length of database: 431 Effective search space: 184899 Effective search space used: 184899 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