Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate BWI76_RS07545 BWI76_RS07545 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Koxy:BWI76_RS07545 Length = 394 Score = 133 bits (335), Expect = 9e-36 Identities = 119/386 (30%), Positives = 180/386 (46%), Gaps = 36/386 (9%) Query: 69 GPLMGLPVSVKDLYGVPGLPVFAGSDE--ALPEAWQAAGPLVARLQRQLGIVVGKTHTVE 126 GPL GL +VKDL+ V G P G+ AL P+V L +GKTHT E Sbjct: 22 GPLSGLTFAVKDLFDVAGYPTGGGNPHLLALSGIKNRTAPVVQTLLNNGARFIGKTHTSE 81 Query: 127 FAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPAS 186 A+ G N H+GTPRN +P+ +PGGSS+G+ ++ ALGTDT GSVR PAS Sbjct: 82 LAYSMSGHNVHYGTPRNGAAPNH--IPGGSSSGSASAVSNEVCDFALGTDTGGSVRTPAS 139 Query: 187 MTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAPVR 246 G GL+ T GR ++G PL +++DT G R+ E + A L + + Sbjct: 140 YCGLFGLRPTHGRLSLDGCQPLCATMDTCGFFARSPEVFSAVAACLFADER-------AD 192 Query: 247 VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQV--VRFPLPHCEEAFDIFRRGG 304 + G+R+ F + A++ QRLA+ V + PLP ++ + FR+ Sbjct: 193 LSGVRLACHDGLF-SRLPLRSQQALQPVRQRLARFFGAVTPLAAPLPDVDDIYLAFRQ-- 249 Query: 305 LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGA---ARL 361 + E + +L VR+R W + V+ ++ A QR A A+L Sbjct: 250 IQGYEAWQAQGETIERYGLQLGSDVRERFFWGKAVTRAQF--DAACQQRVRFAAWWDAQL 307 Query: 362 FDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTA-----ISNLFGWCALTMPVG 416 D VL+ PTVP P L T ++A+R + IS + +T+PV Sbjct: 308 GD--AVLVMPTVPDGAPLL-------TAQAEEIEAVRRLSHDLLLISVMTQRPQVTLPVA 358 Query: 417 LDANRMPVGLQLMGPPRAEARLIGIA 442 +P+G+ +GP ++ L+ +A Sbjct: 359 -QTGGLPLGISFLGPRGSDRLLVELA 383 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: 455 Number of extensions: 26 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: 394 Length adjustment: 32 Effective length of query: 430 Effective length of database: 362 Effective search space: 155660 Effective search space used: 155660 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