Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_015447086.1 R2APBS1_RS04915 amidase
Query= SwissProt::Q38M35 (462 letters) >NCBI__GCF_000230695.2:WP_015447086.1 Length = 537 Score = 119 bits (297), Expect = 3e-31 Identities = 149/496 (30%), Positives = 217/496 (43%), Gaps = 65/496 (13%) Query: 4 AHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLD 63 A L A L R+LT AL+D Q R P L A A + A A+DT Sbjct: 36 AQLQQRMDAGTLDSRQLTQ-ALLDRI-QRIDRSGPTLRAVIE-SNPEALALAGALDTKRT 92 Query: 64 QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAW--QAAGPLVARLQRQLGIVVGK 121 + GPL G+PV +KD + AL +A + AG LV RL++ +V+GK Sbjct: 93 KAH--GPLYGIPVLLKDNIDTGDRMLTTAGSLALIDAPAPRDAG-LVERLRKAGALVLGK 149 Query: 122 THTVEFA-----FGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTD 176 T+ E+A G + G +NP+ R P GSSAG+ ++ G A A+G++ Sbjct: 150 TNLSEWANFRSNHASSGWSGRGGQTKNPYVLD--RNPCGSSAGSAAAVAAGLATAAIGSE 207 Query: 177 TAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTES 236 T GS+ PA+M G VG+K T+G GIVP+S S DTAG + R+V D A + Sbjct: 208 TDGSIICPAAMNGIVGIKPTLGLVSRSGIVPISHSQDTAGPMARSVADAAALLTVIAGSD 267 Query: 237 QGLPAPA--------------PVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAG 282 PA A P ++G R+GV +P+ +E A+ + G Sbjct: 268 PRDPATAEADRHATDYTKFLDPNGLRGKRIGVVRQ--LAGAEPNADRVLEQAIALMKAQG 325 Query: 283 AQVV-RFPLPHCEEAFD-----------------IFRRGGLAASELAAYLDQHFPHKVER 324 A +V LPH E + + R GL A LA + + H E Sbjct: 326 AIIVDPVKLPHLAELGEPEMTVLLYDFKHDIDAYLANRRGLKARTLADLVAFNQAHAGEE 385 Query: 325 LDPVVRDRVRWAEQ---VSSVEYLRRKAVLQRC----GAGAARLFDDVDVLLTPT-VPA- 375 + ++ AE+ +S Y A +R G AA +D LL P+ PA Sbjct: 386 MPWFGQELFEQAEKKGPLSDKAYTDALAKAKRLSGPEGIDAALQAQHLDALLAPSWGPAF 445 Query: 376 -SPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRA 434 + P L D + + P A + A++ G+ ++T+P G A+ +PVG+ L G + Sbjct: 446 MTDPVLGD--HIVSGDPTVGGASQPAAVA---GYPSITVPAGF-AHGLPVGIVLFGAKWS 499 Query: 435 EARLIGIALGIEALIG 450 E LI IA G E G Sbjct: 500 EPALISIAYGFEQHAG 515 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: 585 Number of extensions: 32 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: 537 Length adjustment: 34 Effective length of query: 428 Effective length of database: 503 Effective search space: 215284 Effective search space used: 215284 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 24 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