Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate HSERO_RS09160 HSERO_RS09160 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__HerbieS:HSERO_RS09160 Length = 450 Score = 222 bits (566), Expect = 2e-62 Identities = 159/446 (35%), Positives = 227/446 (50%), Gaps = 16/446 (3%) Query: 9 AEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQDL 68 A H L+ E A+A I A AR+ R+ A +AR+AA A DTL Sbjct: 14 AGHTTSLQLTE-QALARIADPAGEGARVFTRVYA------EQARAAARASDTLRAARLCR 66 Query: 69 GPLMGLPVSVKDLYGVPGLPVFAGSD--EALPEAWQAAGPLVARLQRQLGIVVGKTHTVE 126 PL G+PVSVKDL+ V G AGS P A A +V L + I++GKT+ E Sbjct: 67 SPLEGVPVSVKDLFDVAGETTLAGSVVLRGKPVA-SAHAAVVQNLLKAGAILIGKTNMTE 125 Query: 127 FAFGGLGVNAHWGTPRNPWSPHEH--RVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 FA+ GLG+N H+GTP+N W + R+PGGSS+GA +S+ G A A+G+DT GSVR+P Sbjct: 126 FAYSGLGINPHYGTPQNAWERNIEGGRIPGGSSSGAAISVTDGMAFAAVGSDTGGSVRIP 185 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAP 244 +++ G G K T R ++G++PLS+ LD+ G L +V+ A A L E P Sbjct: 186 SALNGLTGFKPTAARVSMQGVLPLSAYLDSIGPLAVSVQCCAIMDAVLAGEDYVAVLAHP 245 Query: 245 VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGG 304 +R GLR+ PTN D +D ++ A A+ +LA AGA +V +P I +GG Sbjct: 246 LR--GLRLLAPTNVVLDGMDDTVGQAYRTALGKLAAAGAMIVEAEVPAFNALAAINAKGG 303 Query: 305 LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLFDD 364 A+E A+ D V R+ + +S+ + L R A Sbjct: 304 FTAAEAYAWHRALIAENAAGYDQRVVSRILRGKDMSAADLLDVLHARPRWIAQVEAQLAG 363 Query: 365 VDVLLTPTVPASPPRLADI-GTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMP 423 D L+ PTVP PR+A++ + + Y AN K +RN + N CAL++P + P Sbjct: 364 YDALVMPTVPIVAPRIAELQASDDAYYGANGKMLRNPTLINFLDGCALSLPCHAPGS-AP 422 Query: 424 VGLQLMGPPRAEARLIGIALGIEALI 449 VGL L + RL+ I L +EAL+ Sbjct: 423 VGLSLAACGGQDKRLLSIGLAVEALL 448 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: 465 Number of extensions: 23 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: 450 Length adjustment: 33 Effective length of query: 429 Effective length of database: 417 Effective search space: 178893 Effective search space used: 178893 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