Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate CCNA_01906 CCNA_01906 allophanate hydrolase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Caulo:CCNA_01906 Length = 594 Score = 144 bits (363), Expect = 8e-39 Identities = 139/463 (30%), Positives = 203/463 (43%), Gaps = 54/463 (11%) Query: 3 AAHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLL 62 AA ++ + A + R L A+ D ++P++ + + A + A AVD + Sbjct: 12 AAGVNAGDSAESVARSALAAIEAYDA-------IQPQVWTLRLPEAA-VLAQARAVDARI 63 Query: 63 DQGQDLGPLMGLPVSVKDLYGV---------PGLPVFAGSDEALPEAWQAAGPLVARLQR 113 G+ L PL G+P +VKD V PG AG + E AAG Sbjct: 64 AAGETL-PLAGVPFAVKDNIDVADLATTAACPGFAYTAGRSATVVEQLLAAG-------- 114 Query: 114 QLGIVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLAL 173 ++VGKT+ +FA G +G + +G PR ++ + V GGSS+G+ V++ G AL Sbjct: 115 --AVLVGKTNLDQFATGLVGTRSPYGAPRCVFN--QAFVSGGSSSGSAVAVAAGLVAFAL 170 Query: 174 GTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTR------TVEDLAY 227 GTDTAGS RVPA+ VGLK + GRW G+VP SLD V V+ + Sbjct: 171 GTDTAGSGRVPAAFNHLVGLKPSKGRWSTRGLVPACRSLDCISVFAADLDGAGRVDAVLA 230 Query: 228 AFAALDTESQGLPAPAP-VRVQGLRVGVPTNH---FWDDIDPSIAAAVEAAVQRLAQAGA 283 AF D S+ P P P + + GLRV +P F+ D + A +AV RL AGA Sbjct: 231 AFDPEDPYSRPAPQPEPALTLAGLRVAIPRPEQRIFFGDGESE--ALYASAVARLQAAGA 288 Query: 284 QVVRFPLPHCEEAFDIFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVE 343 V + +A + G A AA ++ ++P VR V+ V+ VE Sbjct: 289 VAVEVDMAPLLDAAKLLYSGPWVAERTAA-VEPLLRAAPSAIEPTVRAIVQGGLAVTGVE 347 Query: 344 YLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRN---- 399 R L+ A ++ D L PT P I TV+ + N Sbjct: 348 TFRGLYALEAYRRAAEAVWAAADALFLPTTPT-------IYTVKALKAEPLALNANLGLY 400 Query: 400 TAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 T NL AL +P G A+ G+ +GP A+ L+ +A Sbjct: 401 TNFVNLLDLSALAVPAGFRADGTGFGVTFIGPAFADRALLDLA 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: 612 Number of extensions: 31 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: 594 Length adjustment: 35 Effective length of query: 427 Effective length of database: 559 Effective search space: 238693 Effective search space used: 238693 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: 52 (24.6 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