Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate H281DRAFT_03959 H281DRAFT_03959 aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Burk376:H281DRAFT_03959 Length = 459 Score = 241 bits (615), Expect = 4e-68 Identities = 170/450 (37%), Positives = 240/450 (53%), Gaps = 13/450 (2%) Query: 8 LAEHAARLRRRELTAVALIDTCAQHHARMEPR-LNAYKTWDGARARSAAAAVDTLLDQGQ 66 LA+ AA L T+ AL++T + A + A+ D AR AA A D L G Sbjct: 11 LAQLAADLAAGRTTSRALVETALERIADPAGQGAVAFMHVDADGARQAADAHDRLRAAGT 70 Query: 67 DLGPLMGLPVSVKDLYGVPGLPVFAGSDEAL--PEAWQAAGPLVARLQRQLGIVVGKTHT 124 L PL G+PVSVKDL+ + G P AGS P A Q A VARL+R ++VG+T+ Sbjct: 71 VLSPLAGIPVSVKDLFDIEGQPTRAGSTVLADAPAATQDA-VAVARLKRAGAVIVGRTNM 129 Query: 125 VEFAFGGLGVNAHWGTPRNPWSPH---EHRVPGGSSAGAGVSLVQGSALLALGTDTAGSV 181 EFAF GLG+N H+G P +P+ + R+ GGSS+GA S+ G A +ALGTDT GS+ Sbjct: 130 SEFAFSGLGLNPHYGNPLSPYRRDVKGDERISGGSSSGAAASVADGMAAVALGTDTGGSL 189 Query: 182 RVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPA 241 R+PA++ G G K T R P +G VPLS +LD+ G + +V A L +PA Sbjct: 190 RIPAALCGLTGFKPTAARVPKQGGVPLSPTLDSFGPIGVSVACCALVDRMLAGLEPRVPA 249 Query: 242 PAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFR 301 P ++G+R+GV TN+ D ++P +AAAV+ A++ L AGA V + DI Sbjct: 250 ARP--LEGVRLGVLTNYVTDGVEPEVAAAVDTALKHLEAAGAIVSEVRFASLDRLPDI-N 306 Query: 302 RGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAAR- 360 R G + E A+ E+ DP V R+ + S+ +YL A A AAR Sbjct: 307 RFGFSPIEAYAWHRPLLEKHREQYDPRVLVRILKGQPASAADYLDLLAERDAMLAEAART 366 Query: 361 LFDDVDVLLTPTVPASPPRLAD-IGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDA 419 L+ D ++ PTVP PPR+A+ + + + N +RN + N CAL++P L Sbjct: 367 LWQRFDAVVAPTVPMLPPRVAELVSDDDLFGRTNALMLRNPGVFNFLDACALSLPCHLRG 426 Query: 420 NRMPVGLQLMGPPRAEARLIGIALGIEALI 449 + PVGL L G P A+ L+ I G EA++ Sbjct: 427 D-APVGLMLAGAPHADDALLAIGRGAEAVL 455 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: 544 Number of extensions: 34 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: 459 Length adjustment: 33 Effective length of query: 429 Effective length of database: 426 Effective search space: 182754 Effective search space used: 182754 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