Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate RR42_RS09095 RR42_RS09095 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Cup4G11:RR42_RS09095 Length = 447 Score = 227 bits (578), Expect = 7e-64 Identities = 154/444 (34%), Positives = 232/444 (52%), Gaps = 19/444 (4%) Query: 14 RLRRRELTAVALIDTCAQHHARMEPRLNA---YKTWDGARARSAAAAVDTLLDQGQDLGP 70 RLR ++ +I AQH +P +A + T+D A A A D G+ L P Sbjct: 11 RLRDGAISRADVIAQAAQH--AQQPDAHAVFLHTTFD--TAAQVAKAADAATRAGKPLHP 66 Query: 71 LMGLPVSVKDLYGVPGLPVFAGS---DEALPEAWQAAGPLVARLQRQLGIVVGKTHTVEF 127 L GLPVSVKDL+ + G AGS +AL A A +V RL+ +VG+T+ EF Sbjct: 67 LAGLPVSVKDLFNIAGEASRAGSPVRSDAL--AATADATVVRRLRESGAALVGRTNMTEF 124 Query: 128 AFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPASM 187 AF G+G+N H+GTP NP R+PGGSS+GA VS+ G A+ LG+DT GS+R+PA++ Sbjct: 125 AFSGVGINPHFGTPVNPADKQVARIPGGSSSGAAVSVALGLAVAGLGSDTGGSIRIPAAL 184 Query: 188 TGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAPVRV 247 G G K T R P++G PLS +LDTA + RTV+D + + ++ P Sbjct: 185 CGLTGFKPTARRVPLDGAFPLSYTLDTACAMARTVQDCVLVDSVIADQA---VLPVIKAA 241 Query: 248 QGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRGGLAA 307 G+R+ +P D +D ++A A + A+ RL+ AG Q+ LP E I GG A Sbjct: 242 AGIRLAIPRQVLLDGLDDTVARAFDRALGRLSAAGVQIEHIDLPELAELASINAGGGFTA 301 Query: 308 SELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYL-RRKAVLQRCGAGAARLFDDVD 366 +E A + E+ DP V R+ +S+ +Y+ +A L AAR+ + D Sbjct: 302 AEAHAIHRHVLATRREQYDPRVASRIDRGAAMSAADYVDLMRARLDWIARVAARI-EGFD 360 Query: 367 VLLTPTVPASPPRLADIGTVET-YAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVG 425 + PTVP P +A + + + N +RNT+ N C++++P + +PVG Sbjct: 361 AVTCPTVPMVAPPIAPLVADDALFFRTNALLLRNTSAFNFLDGCSISLPCH-QPDELPVG 419 Query: 426 LQLMGPPRAEARLIGIALGIEALI 449 L L +A+L+G A+ +E++I Sbjct: 420 LMLSHGALRDAQLLGTAIALESII 443 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: 461 Number of extensions: 19 Number of successful extensions: 4 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: 447 Length adjustment: 33 Effective length of query: 429 Effective length of database: 414 Effective search space: 177606 Effective search space used: 177606 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