Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate PfGW456L13_3117 putative amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3117 Length = 446 Score = 165 bits (417), Expect = 3e-45 Identities = 141/453 (31%), Positives = 216/453 (47%), Gaps = 25/453 (5%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWD--GARARSAAAAVDTLLD 63 +++ + A RLR+ T LI++ A + +AY D RA + A A Sbjct: 2 ITMMQTAERLRQGLTTPDKLIES-----ALAAIKNSAYVFIDVLEQRAFNDAEASTRRWR 56 Query: 64 QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIV-VGKT 122 QG L P G+P +VKDL V G AGS + V LG++ +GKT Sbjct: 57 QGAPLSPFDGIPYAVKDLLDVVGSRTTAGSITRIDAPMAVEDAEVIAALAALGMIPLGKT 116 Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182 + EFA+ GLG+N H+GTP + E RVPGGSS+G+ +++ +G A+GTDTAGS+R Sbjct: 117 NLTEFAYSGLGLNPHFGTPTCDVAVSESRVPGGSSSGSAIAVQRGIVTCAIGTDTAGSIR 176 Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLP-- 240 +PA+ G VG K + R+ ++G+ PL+ +LD+ G TV D ALD +G Sbjct: 177 IPAAFNGLVGYKASTSRYSMKGLHPLAITLDSLGPFAHTVADC----VALDAAMRGFKNV 232 Query: 241 APAPVRVQGLRVGVPTNHFWDD-IDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFD- 298 A V + LR V D + P + + + ++RL AGAQV R P+ + Sbjct: 233 AIEAVNLSSLRFVVDDGVMSDPALQPVVQHNLVSMMERLRAAGAQVERRPVLAVARTREL 292 Query: 299 IFRRGGLAASE----LAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRC 354 I R G L A E L A ++ H+++R VR R+R A++V R + + Sbjct: 293 IVREGWLGAIEAWRLLGAIVEGPQGHQMDRR---VRHRLRAAKEVDPASEARIRHLRTEL 349 Query: 355 GAGAARLFDDVDVLLTPTVPASPPRLADIGT-VETYAPANMKAMRNTAISNLFGWCALTM 413 A R D +L+ PTV P +A + E +A N++ + T I +L + + Sbjct: 350 MAAMERELDGA-ILVMPTVKHVAPPMAPLSNDDELFASVNLETLSLTMIGSLLDMPGVAI 408 Query: 414 PVGLDANRMPVGLQLMGPPRAEARLIGIALGIE 446 P G D+ + + +L+ L IE Sbjct: 409 PSGKDSIGLATSTLFSTTQGRDDQLLSACLAIE 441 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: 415 Number of extensions: 24 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: 446 Length adjustment: 33 Effective length of query: 429 Effective length of database: 413 Effective search space: 177177 Effective search space used: 177177 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