Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate 3606629 Dshi_0061 Amidase (RefSeq)
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Dino:3606629 Length = 443 Score = 204 bits (518), Expect = 6e-57 Identities = 153/418 (36%), Positives = 205/418 (49%), Gaps = 23/418 (5%) Query: 38 PRLNAYKTWDGARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEAL 97 PR+ A T D A + A AA D Q + GPL G+P+S KDL+ G+ +G+ Sbjct: 42 PRIYARTTPDRALSE-AMAAHDRARSQTRH-GPLDGVPISWKDLFDTAGVATESGTALLK 99 Query: 98 PEAWQAAGPLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSS 157 ++A + +GKTH E AF GLG+N TP N P VPGGSS Sbjct: 100 GRTPDRDAEVLANATAAGLVCLGKTHLSELAFSGLGLNPITATPPNINDPGA--VPGGSS 157 Query: 158 AGAGVSLVQGSALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGV 217 +GA S+ G A +G+DT GSVR+P++ VGLKTT G +EG VPL+S+ DT G Sbjct: 158 SGAAASVAFGLAAAGIGSDTGGSVRIPSAWNDLVGLKTTSGLLSLEGAVPLASAFDTVGP 217 Query: 218 LTRTVEDLAYAFAALDTESQGLPAP--APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAV 275 LTRTVED A AL G AP + G + V ++DI P A AAV Sbjct: 218 LTRTVEDAALLLGALG----GTKAPDLRGATLTGTHLAVLRTGAFEDIRPEPEQAFAAAV 273 Query: 276 QRLAQAGAQVVRFPLPHCEEAFDIFRRGGLAASELAAYLDQHFPHKVERLDPVVRDRVRW 335 RLA+AGAQ+ P +EA + G L A+E E++ P + DR R Sbjct: 274 ARLAEAGAQITELHAPEVDEALAL--SGVLFATEAYGIWKDVIEAAPEKMFPPILDRFRG 331 Query: 336 AEQVSSVEYL---RRKAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETY-AP 391 + Y+ R+ L+ A R FD V L PT P PP + + + + Y Sbjct: 332 GRDYDAPAYVAGWRKLVELRAVWADRTRAFDGV---LLPTAPTLPPNVDRLLSEKAYFVE 388 Query: 392 ANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALI 449 N+ A+RNT I NL G CAL +P G + GL +MG P EA L+ + EA + Sbjct: 389 ENLLALRNTRIGNLMGVCALNLPTGTPS----CGLSIMGQPFGEAALLRLGAAAEAAL 442 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: 503 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 462 Length of database: 443 Length adjustment: 33 Effective length of query: 429 Effective length of database: 410 Effective search space: 175890 Effective search space used: 175890 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