Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate GFF1036 PS417_05250 hypothetical protein
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__WCS417:GFF1036 Length = 434 Score = 179 bits (455), Expect = 1e-49 Identities = 133/408 (32%), Positives = 206/408 (50%), Gaps = 20/408 (4%) Query: 50 RARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSD--EALPEAWQAAGPL 107 RAR A A GQ L G+P++ KDL+ V G AG+ P A A P Sbjct: 37 RARREAEAAAARWRAGQPLSVFDGVPLAWKDLFDVAGSITTAGAAYRRNAPAALLDA-PT 95 Query: 108 VARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQG 167 V L R + VGKT+ E A+ GLG+N H+GTP NP + R+PGGSS+G+ V++ Sbjct: 96 VGLLCRAGMVSVGKTNLSELAYSGLGLNPHFGTPHNPHGTDQPRIPGGSSSGSAVAVAAA 155 Query: 168 SALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAY 227 +A+GTDTAGS+R+P++ G VG +++ R+ +G+ PL+ +LD+ G LTR+V D Sbjct: 156 IVPIAMGTDTAGSIRIPSAFNGLVGYRSSSRRYSRDGVFPLAHTLDSLGPLTRSVRDA-- 213 Query: 228 AFAALDTESQGLPAPAPVR-VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVV 286 A+D G R ++G R + D++P++ + AV++L GA + Sbjct: 214 --LAIDDLLHGRRQTHIARSLKGQRFVLAQ----QDVEPAVRNNLLRAVEQLKAHGALIE 267 Query: 287 RFPLPHCEEAFDIFRRGGLAASELAAYLDQHF--PHKVERLDPVVRDRVRWAEQVSSVEY 344 P + D+ + G S A L + E+LDP VR R+ A + + + Sbjct: 268 ERECPTFQATLDLIKHHGWLGSFEAFALHEALLDSPDAEQLDPRVRRRLEAARALPASQL 327 Query: 345 LRRKAVLQRCGAGAARLFDDVD--VLLTPTVPASPPRLADI-GTVETYAPANMKAMRNTA 401 L +R +L D+D +L+TPT+ P LA + E + N+ +R T Sbjct: 328 LHLFDARRRL---QQQLMADLDGALLITPTIAHVAPALAPLEADDELFVKTNLATLRLTM 384 Query: 402 ISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALI 449 +L +T+P G DA +P GL L P +ARL+ AL +E+++ Sbjct: 385 PGSLLDMPGVTLPSGRDAQGLPTGLLLSAPAGEDARLLRAALSVESVL 432 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: 507 Number of extensions: 35 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: 434 Length adjustment: 33 Effective length of query: 429 Effective length of database: 401 Effective search space: 172029 Effective search space used: 172029 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