Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate PP_0931 PP_0931 Glutamyl-tRNA(Gln) amidotransferase subunit A
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Putida:PP_0931 Length = 483 Score = 167 bits (424), Expect = 5e-46 Identities = 140/470 (29%), Positives = 215/470 (45%), Gaps = 40/470 (8%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 L+LAE A L + ++ L +++P++N++ + A A A D G Sbjct: 4 LTLAEIARGLADKSFSSEELTGALLARIKQLDPQINSFISVTEDLALGQARAADARRAAG 63 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125 + L+G P++ KDL+ G+ GS +VA+L + +GKT+ Sbjct: 64 ET-SALLGAPIAHKDLFCTNGVRTSCGSKMLDNFKAPYDATVVAKLAEAGMVTLGKTNMD 122 Query: 126 EFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPA 185 EFA G ++H+G +NPW+ EH VPGGSS G+ ++ GTDT GS+R PA Sbjct: 123 EFAMGSANESSHYGAVKNPWNL-EH-VPGGSSGGSAAAVAARLLPATTGTDTGGSIRQPA 180 Query: 186 SMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAY------AFAALDTESQGL 239 ++T GLK T GR G++ +SSLD G L RT ED A F A D+ S Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALLLQGMAGFDAKDSTSIEE 240 Query: 240 PAP-----APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCE 294 P P +QGLR+G+P +F +DP IA V+A+V+ L + GA V LP+ + Sbjct: 241 PVPDYSASLNASLQGLRIGLPKEYFGAGLDPRIADLVQASVKELEKLGAVVKEISLPNMQ 300 Query: 295 EAFDIFR--RGGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVE--------- 343 A + A+S L+ + F ++ E + R + VE Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEEPKDLTDLYKRSRGEGFGVEVQRRIMVGT 360 Query: 344 -----------YLRRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPA 392 Y++ + + + F+DVD++L PT P +L G + A Sbjct: 361 YALSAGYYDAYYVKAQQIRRLIKNDFMAAFNDVDLILGPTTPNPAWKL---GAKSSDPVA 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: 444 Number of extensions: 21 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 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