Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Dsui_0886 Dsui_0886 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__PS:Dsui_0886 Length = 489 Score = 174 bits (442), Expect = 4e-48 Identities = 144/478 (30%), Positives = 224/478 (46%), Gaps = 53/478 (11%) Query: 7 SLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQ 66 SL E A L +++++V L R+ P +NAY + R+ + A A D L G Sbjct: 5 SLKELAQALAGKKISSVELTQLYLDRINRLNPAINAYVSTQPERSLAQAKAADARLAAG- 63 Query: 67 DLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTVE 126 D GPL G+P++ KD++ G GS ++ + + +GKT+ E Sbjct: 64 DAGPLTGIPLAQKDIFCAEGWLTTCGSKMLANFVSPYDATVIQKFDAAGAVNLGKTNMDE 123 Query: 127 FAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPAS 186 FA G + +G +NPW + RVPGGSS G+ ++ A A GTDT GS+R PA+ Sbjct: 124 FAMGSSNETSFFGPVKNPWD--QSRVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQPAA 181 Query: 187 MTGQVGLKTTVG---RWPVEGIVPLSSSLDTAGVLTRTVED---LAYAFAALDTE----- 235 + GLK T G RW G++ +SSLD AG + R+ ED L A A D + Sbjct: 182 LCNLTGLKPTYGVVSRW---GMIAFASSLDQAGPMARSAEDCGLLLNAMAGFDPKDSTSL 238 Query: 236 -------SQGLPAPAPVR-VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVR 287 ++ L APA + + GL+VG+P F + D ++ AA++AA+++ GA++V Sbjct: 239 ERPVEDYTRELNAPASAKPLAGLKVGLPKEFFGEGCDAAVMAAIQAAIEQYKALGAEMVE 298 Query: 288 FPLPH-------------CEEAFDIFR----RGGLAASELAAYLDQHFPHKVERLDPVVR 330 LP+ E + ++ R R G ASE + D + + + V+ Sbjct: 299 VSLPNMKLSVPAYYVIAPAEASSNLSRFDGVRYGYRASEYDSLDDMYAKSRAQGFGAEVK 358 Query: 331 DRVRWAEQVSS-----VEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGT 385 R+ V S YL+ + + + F DV+L PT P++ +L D Sbjct: 359 RRILIGTYVLSHGYYDAYYLQAQRIRRLIAEDFVAAFKQCDVILGPTSPSTAFKLGD--- 415 Query: 386 VETYAPANMKAMRNTAIS-NLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 + P M I+ NL G +++P G A +PVGLQL+G EARL+ +A Sbjct: 416 -KAGDPVQMYLSDIYTIAVNLAGLPGMSLPCGF-AEGLPVGLQLIGNYFDEARLLNVA 471 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: 476 Number of extensions: 30 Number of successful extensions: 7 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: 489 Length adjustment: 33 Effective length of query: 429 Effective length of database: 456 Effective search space: 195624 Effective search space used: 195624 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