Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate N515DRAFT_0701 N515DRAFT_0701 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Dyella79:N515DRAFT_0701 Length = 541 Score = 120 bits (300), Expect = 1e-31 Identities = 128/435 (29%), Positives = 198/435 (45%), Gaps = 61/435 (14%) Query: 62 LDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEAL---PEAWQAAGPLVARLQRQLGIV 118 +D+ + G L G+PV +KD + AL P A + AG LVARL++ ++ Sbjct: 86 IDRQKPKGALRGIPVLLKDNIDTGDRMLTTAGSLALADAPPAPRDAG-LVARLRKNGALI 144 Query: 119 VGKTHTVEFA-----FGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLAL 173 +GKT+ E+A G +A G RNP++ R P GSSAG+G ++ G A +A+ Sbjct: 145 LGKTNLSEWANMRSNHASSGWSARGGQTRNPYALD--RNPCGSSAGSGAAVAAGLATVAI 202 Query: 174 GTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALD 233 G++T GS+ PA+ G VG+K TVG GIVP+S + DTAG + RTV D A A+ Sbjct: 203 GSETDGSIICPAAANGIVGIKPTVGLVSRSGIVPISHNQDTAGPMARTVADAAAVLGAIA 262 Query: 234 TESQGLPAPA--------------PVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLA 279 PA A P ++G R+GV +P+ +E ++ + Sbjct: 263 GSDPRDPATAEADKHATDYTRFLDPNGLKGKRIGVVRG--LAGAEPNADRILEQSIALMK 320 Query: 280 QAGAQVV-RFPLPHCEEAFDIFRRGGL--AASELAAYLDQHFPHKVERLDPVVRDRVRWA 336 GA +V LPH +E D L ++ AYL ++ L ++ R A Sbjct: 321 AQGAVIVDPVELPHLKELGDPELTVLLYDLKQDMQAYLATRTGTSMKTLADLIAFNKREA 380 Query: 337 EQ------------------VSSVEYLRRKAVLQRC----GAGAARLFDDVDVLLTPT-- 372 E+ ++ +Y+ +A +R G A D +D LL P+ Sbjct: 381 EREMPWFGQELFEQAQAKGPLTDKDYVEAQAKAKRFAGPEGIDVALAKDHLDALLAPSWG 440 Query: 373 -VPASPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGP 431 + P L D V + P A + A++ G+ ++T+P G A+ +PVG+ G Sbjct: 441 PTFVTDPVLGD--HVVSGDPTVGGASQPAAVA---GYPSITVPAGF-AHDLPVGIVFFGA 494 Query: 432 PRAEARLIGIALGIE 446 +E LI IA G E Sbjct: 495 KWSEPTLITIAYGYE 509 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: 594 Number of extensions: 30 Number of successful extensions: 3 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: 541 Length adjustment: 34 Effective length of query: 428 Effective length of database: 507 Effective search space: 216996 Effective search space used: 216996 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: 52 (24.6 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