Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate AO353_15115 AO353_15115 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15115 Length = 462 Score = 162 bits (410), Expect = 2e-44 Identities = 148/469 (31%), Positives = 216/469 (46%), Gaps = 40/469 (8%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 L+ AE AR R+LT + D H R EP++NA +D + R A A ++G Sbjct: 7 LTAAELLARFASRQLTPIDYYDQLLTHIDRWEPQINALYAFDPQQVRQQAQASTERWNKG 66 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125 Q G L G+PV++K+L G P+ GS P ARL+ I++ KT Sbjct: 67 QPNGALDGVPVTLKELIATEGQPIPLGSAATRLTPALKDAPPAARLREAGAIILAKTTVP 126 Query: 126 EFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPA 185 +F G+++ G RNPW+ + PGGSSAGA + G L +GTD GSVR+PA Sbjct: 127 DFGMLSSGLSSFHGITRNPWNTANN--PGGSSAGAAAAAAAGYGPLHVGTDIGGSVRLPA 184 Query: 186 SMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAAL----DTESQGLP- 240 + G VG K T+GR P++ P + TAG +TRTV+D L ++ LP Sbjct: 185 AWCGLVGFKPTLGRIPID---PYYTG-RTAGPMTRTVDDCVLLMQHLARPDSRDATSLPP 240 Query: 241 -----APAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAV-------QRLAQAGAQVVRF 288 + P+ V+GLRVG+ ++P A EA V RL +A V Sbjct: 241 LTTPWSNQPLSVKGLRVGLM-------LEPGAGLAPEAFVCNAVEQAARLFEAHGAKVTV 293 Query: 289 PLPHCEEA----FDIFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEY 344 P + A D F R A EL+A + F +R+ P +RD ++ VE Sbjct: 294 IAPIMDRAQLDGLDQFWRARQWA-ELSALSSEQF----DRVLPYIRDWAAPGADITGVEA 348 Query: 345 LRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTAISN 404 +R AA+LFD D++L+PT + AD + + + T N Sbjct: 349 VRGFNQTFEMRRRAAQLFDTFDLVLSPTNQIN-AFAADWPSPSNDPQQPFEHIVFTVPWN 407 Query: 405 LFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALIGQGH 453 + AL++ G A+ MP+GLQ++ P A+ L+ IA E G H Sbjct: 408 MGEQPALSINCGFAADGMPIGLQMIAPRFADQWLLQIAKTYENWRGAIH 456 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: 507 Number of extensions: 30 Number of successful extensions: 6 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: 462 Length adjustment: 33 Effective length of query: 429 Effective length of database: 429 Effective search space: 184041 Effective search space used: 184041 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