Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Pf1N1B4_1101 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__pseudo1_N1B4:Pf1N1B4_1101 Length = 483 Score = 175 bits (443), Expect = 3e-48 Identities = 142/470 (30%), Positives = 218/470 (46%), Gaps = 40/470 (8%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 L+LAE A L ++ ++ L A+++P+LN++ + A A A D G Sbjct: 4 LTLAEIARGLADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALQQAKAADARRANG 63 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125 + G L+G P++ KDL+ G+ GS +VA+L + +GKT+ Sbjct: 64 ES-GALLGAPIAHKDLFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTNMD 122 Query: 126 EFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPA 185 EFA G ++++G +NPW+ EH VPGGSS G+ ++ A GTDT GS+R PA Sbjct: 123 EFAMGSANESSYYGAVKNPWNL-EH-VPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPA 180 Query: 186 SMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAAL----DTESQGLPA 241 ++T GLK T GR G++ +SSLD G L RT ED A + +S + Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCAILLQGMAGFDPQDSTSIDE 240 Query: 242 PAP-------VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCE 294 P P +QGLR+GVP +F +DP IA V A+V+ L + GA V LP+ + Sbjct: 241 PVPDYSAGLNGSLQGLRIGVPKEYFSAGLDPRIADLVMASVEELKKLGAVVKEISLPNMQ 300 Query: 295 EAFDIFR--RGGLAASELAAYLDQHFPHKV---------------ERLDPVVRDRVRWAE 337 A + A+S L+ + F ++ E P V+ R+ Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEDPKNLEDLYKRSRGEGFGPEVQRRIMVGA 360 Query: 338 QVSS-----VEYLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPA 392 S YL+ + + + F++VD++L PT P +L G + A Sbjct: 361 YALSAGYYDAYYLKAQKIRRLIKNDFMAAFNEVDIILGPTTPNPAWKL---GAKNSDPVA 417 Query: 393 NMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIA 442 T +NL G L+MP G + +PVG+QL+ P E RL+ +A Sbjct: 418 AYLEDVYTITANLAGLPGLSMPAGF-VDGLPVGVQLLAPYFQEGRLLNVA 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: 472 Number of extensions: 25 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