Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate GFF3266 Psest_3329 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__psRCH2:GFF3266 Length = 483 Score = 174 bits (441), Expect = 6e-48 Identities = 145/473 (30%), Positives = 218/473 (46%), Gaps = 44/473 (9%) Query: 5 HLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQ 64 +L+LAE A L + +A L T +++P+LN++ + A + A A D Sbjct: 3 NLTLAEIARNLAEKRFSAEELTRTLLARIEQLDPQLNSFISVTDELAIAQAKAADARRAA 62 Query: 65 GQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHT 124 G+ G L+G P+ KDL+ G+ GS +V RL + +GK + Sbjct: 63 GES-GALLGAPIGHKDLFCTQGIRTSCGSKILDNFKAPYNATVVERLAAAGTVTLGKLNM 121 Query: 125 VEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184 EFA G ++++G +NPW P RVPGGSS G+ ++ A GTDT GS+R P Sbjct: 122 DEFAMGSANESSYYGPVKNPWDPS--RVPGGSSGGSAAAIAARLLPAATGTDTGGSIRQP 179 Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAY------AFAALDTESQG 238 A++T GLK T GR G+V +SSLD G + RT ED A F A D+ S Sbjct: 180 AALTNLTGLKPTYGRVSRWGMVAYASSLDQGGPMARTAEDCALLLSAMAGFDAKDSTSVD 239 Query: 239 LP-----APAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHC 293 P A + GLR+G+P +F +DP IA AV A+V+ L + GA V LP+ Sbjct: 240 QPLDDYLAALSQPLAGLRIGLPKEYFGAGLDPKIADAVMASVEELKKLGATVKDISLPNM 299 Query: 294 EEAFDIFR--RGGLAASELAAYLDQHFPHK----VERLDPVVRDRVR-WAEQVS------ 340 + A + A+S L+ + F ++ V+ D R R + ++V Sbjct: 300 QHAIPSYYVIAPAEASSNLSRFDGVRFGYRCENPVDLTDLYKRSRAEGFGDEVKRRIMVG 359 Query: 341 ---------SVEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLAD--IGTVETY 389 YL+ + + + F+ VD++L PT P +L + V Y Sbjct: 360 TYALSAGYYDAYYLKAQKIRRLIKQDFVTAFEQVDLILGPTTPNLAWKLGEKNADPVSAY 419 Query: 390 APANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 T +NL G L+MP G + +PVG+QL+ P EARL+ +A Sbjct: 420 LEDIY-----TITANLAGIPGLSMPAGF-IDGLPVGVQLLAPYFQEARLLNVA 466 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: 479 Number of extensions: 26 Number of successful extensions: 8 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: 483 Length adjustment: 33 Effective length of query: 429 Effective length of database: 450 Effective search space: 193050 Effective search space used: 193050 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