Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate AZOBR_RS31530 AZOBR_RS31530 glutamyl-tRNA amidotransferase subunit A
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__azobra:AZOBR_RS31530 Length = 462 Score = 224 bits (572), Expect = 4e-63 Identities = 156/449 (34%), Positives = 225/449 (50%), Gaps = 9/449 (2%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 L+L E A +R L A AL D C AR+ P LNA+ + + A +AA A D + G Sbjct: 7 LTLTEAARAVRDGTLRAEALADACLDRIARLNPTLNAFLSVEPEEALAAARAADAEVRAG 66 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAW-QAAGPLVARLQRQLGIVVGKTHT 124 + GPL G+P++ KD++ G GS + + ++ RL + +G H Sbjct: 67 RLRGPLHGVPLAHKDMFHRAGKRCTCGSPTIRGDFRPERTATVLERLDTAGAVTLGTLHM 126 Query: 125 VEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 EFA G G NAH G RNPW P R+ GGSS+G+G ++ A +LG+DT GSVR+P Sbjct: 127 AEFAMGPTGHNAHLGRCRNPWDPD--RITGGSSSGSGAAVAGRLAFGSLGSDTGGSVRLP 184 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAP 244 A++ G VGLK T G P++G++PLS SLD G L R+ ED A F+ + + + A Sbjct: 185 AALCGVVGLKPTQGATPMDGVMPLSESLDCVGPLARSAEDAATLFSVITGRTDAVAAIGQ 244 Query: 245 VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGG 304 V+GLR+G+P ++D +DP++AAA+E A L +AGA+VV +P E D+ Sbjct: 245 -GVEGLRLGIPRQFYYDGLDPAVAAALERARAVLERAGARVVDVDIPDHEPYGDLANL-- 301 Query: 305 LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAV-LQRCGAGAARLFD 363 + E AA + + P VR R+ V + YL+ K + A F Sbjct: 302 VFTPEAAAVHAPWLRERPQDYGPQVRARLLQGLMVPAASYLQAKQLRALHLRAMIDGPFA 361 Query: 364 DVDVLLTPTVPASPPRLA--DIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANR 421 D L P + + P A D+G A T + G AL P G D + Sbjct: 362 RCDALFVPALRSRVPTAAQTDVGAGPAMAAVVAGVAALTRPVSYLGLPALVTPAGFDPDG 421 Query: 422 MPVGLQLMGPPRAEARLIGIALGIEALIG 450 MP+ +QL+ P+AEA L+ IA E G Sbjct: 422 MPIAMQLIARPQAEATLLRIADAYERAAG 450 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: 525 Number of extensions: 32 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: 462 Length adjustment: 33 Effective length of query: 429 Effective length of database: 429 Effective search space: 184041 Effective search space used: 184041 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