Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate 3610038 Dshi_3419 Amidase (RefSeq)
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Dino:3610038 Length = 441 Score = 168 bits (426), Expect = 3e-46 Identities = 138/454 (30%), Positives = 214/454 (47%), Gaps = 31/454 (6%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 LSL + +A LR E+TA+AL+D A +P + A+ D +AR+ A A+D +G Sbjct: 10 LSLQQMSAALRTGEVTALALLDAHLDRIAARDPSVKAWAWLDPDQARAQAIALDAAQAEG 69 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125 + LGPL G+PV +KD+ +P G+ + ARL+ ++VGKT T Sbjct: 70 KALGPLHGIPVGLKDVIDTADMPTENGTPPDAGRQPDQDAWITARLRAVGAVIVGKTTTT 129 Query: 126 EFAFGGLGVNAHWGTPRNPWSPHE-HRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 E AF P +PH + PGGSSAG+ S+ G LA+GT T GSV P Sbjct: 130 ELAFLN---------PTETLNPHNPNHTPGGSSAGSAASVAAGMVPLAVGTQTGGSVIRP 180 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAA-LDTESQGLPAPA 243 A+ G VG+K T G P +G+ S +LDT GV TR ED A+A +DTE Sbjct: 181 AAFCGVVGVKPTFGAIPRQGVTMQSHTLDTLGVFTRDAEDAAFALTCMMDTEDSDPATLP 240 Query: 244 PVRVQGLRVGVPTNHFWDDIDP----SIAAAVEAAVQRLAQA-GAQVVRFPLPHCEEAFD 298 P G + + P +A +AA+++LAQA GA + P E+ D Sbjct: 241 PQDAHPAIAGATRPPVFGFVRPPEWDRASAETKAALEKLAQALGAIPLSLP-ESFEQVAD 299 Query: 299 IFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGA 358 + R + +E+A + ++ + L RD + ++V+YL + A Sbjct: 300 L--RARINFAEMAWHYSRYRTAGWDALSAATRDAMEAGAACAAVDYLAALMQREPLYASL 357 Query: 359 ARLFDDVDVLLTPT-VPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGL 417 LF VD LL P+ + A+P L+ G A+ N + G +T+P+ Sbjct: 358 DPLFSQVDCLLCPSALGAAPEGLSSTG----------DAIFN-GLWTFMGTPCVTLPLPE 406 Query: 418 DANRMPVGLQLMGPPRAEARLIGIALGIEALIGQ 451 +P+G+QL+G + L+ A+ ++ +G+ Sbjct: 407 TEKGLPIGVQLVGRRGEDRALLSKAIWLQGHMGK 440 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: 489 Number of extensions: 18 Number of successful extensions: 5 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: 441 Length adjustment: 33 Effective length of query: 429 Effective length of database: 408 Effective search space: 175032 Effective search space used: 175032 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