Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Ac3H11_3338 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3338 Length = 497 Score = 170 bits (431), Expect = 9e-47 Identities = 146/488 (29%), Positives = 216/488 (44%), Gaps = 67/488 (13%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQH---HARMEPRLNAYK------TWDGARARSAAA 56 L +A+ A LR R ++AV AQH A+ L AY T ARA+ AA Sbjct: 9 LGVAQLATELRERRVSAVE----AAQHFLDRAQAHQNLGAYVAVNPEITLAQARAQDAAI 64 Query: 57 AVDTLLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLG 116 A T GPL G+P++ KD++ G P AGS +V +L Sbjct: 65 AAGTA-------GPLAGVPIAHKDIFVTKGFPSTAGSKMLAGYQSPFDATVVTKLADAGA 117 Query: 117 IVVGKTHTVEFAFGGLGVN---AHWGTP-----RNPWSPHEHRVPGGSSAGAGVSLVQGS 168 + +GK + EFA G N A GT RNPW+ R+PGGSS G+ V++ Sbjct: 118 VTLGKLNCDEFAMGSANENSAVAPVGTDAPAPVRNPWATD--RIPGGSSGGSAVAVAARL 175 Query: 169 ALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYA 228 A GTDT GS+R PAS G G+K T GR G++ +SSLD AG + R+ ED A Sbjct: 176 APAVTGTDTGGSIRQPASFCGITGIKPTYGRASRYGMIAFASSLDQAGPMARSAEDCALL 235 Query: 229 FAAL-----DTESQGLPAPAP-------VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQ 276 +A+ D +S L PA ++GLR+G+P F + + P + AAV+ A++ Sbjct: 236 LSAMCGPDPDRDSTSLDVPAENFSAKLNDSIEGLRIGIPAEFFGEGLAPDVRAAVDGALK 295 Query: 277 RLAQAGAQVVRFPLPHCEEAFDIFR-----------------RGGLAASELAAYLDQHFP 319 + GA++V LP + + ++ + G A + + +D + Sbjct: 296 EYEKLGAKLVPISLPRTQLSIPVYYIIAPAEASSNLSRFDGVKFGHRAKDYSDLVDMYKK 355 Query: 320 HKVERLDPVVRDRVRWAEQVSS-----VEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVP 374 + E V+ R+ V S YL+ + + + F D++ P P Sbjct: 356 TRAEGFGDEVKRRIMIGAYVLSHGYYDAYYLQAQKIRRMIADDFQNAFKSCDLIAGPVAP 415 Query: 375 ASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRA 434 +L D G A+ A T +L G +++P G MPVGLQL+G Sbjct: 416 TVAWKLGDHGNDPL---ADYLADIFTLPGSLAGLPGMSVPAGFGEGGMPVGLQLLGNYFQ 472 Query: 435 EARLIGIA 442 EARL+ A Sbjct: 473 EARLLNAA 480 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: 539 Number of extensions: 32 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: 497 Length adjustment: 34 Effective length of query: 428 Effective length of database: 463 Effective search space: 198164 Effective search space used: 198164 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