Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate AO356_09120 AO356_09120 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09120 Length = 453 Score = 192 bits (488), Expect = 2e-53 Identities = 150/439 (34%), Positives = 227/439 (51%), Gaps = 24/439 (5%) Query: 23 VALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLY 82 V +++ + AR E + + + ARAR A A GQ L G+P++ KDL+ Sbjct: 24 VQVLEQALEQAARAE---HVFVSLTEARARREAQASAARWRAGQPLSGFDGVPMAWKDLF 80 Query: 83 GVPGLPVFAGSD---EALPEAWQAAGPLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWG 139 V G A + A P AA V+ L R + +GKT+ EFA+ GLG+N H+G Sbjct: 81 DVAGSVTTAAAAVRRNAPPALLDAAS--VSLLSRAGMVCLGKTNLSEFAYSGLGLNPHFG 138 Query: 140 TPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPASMTGQVGLKTTVGR 199 TP NP+S + R+PGGSS+G+ V++ G +A+GTDTAGS+RVPA+ VG + + R Sbjct: 139 TPVNPFSDAQPRIPGGSSSGSAVAVAAGIVPIAMGTDTAGSIRVPAAFNALVGFRASSRR 198 Query: 200 WPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAPVRVQGLRVGVPTNHF 259 +G+ PL+ S+D+ G LTR+V D A+ L AP + G R V Sbjct: 199 HNRDGVFPLAHSIDSIGPLTRSVRD-AWMIDELLQGRDPRQAPPVRSLAGQRFWVEQAVL 257 Query: 260 WD-DIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFR-RGGLAASELAAYLDQH 317 D ++ ++ A V A VQ L AGA V PLP + + + R G L A+E A + Sbjct: 258 EDARVEAAVRANVLAGVQALRTAGALVEIRPLPAFQASLALIRDHGWLGAAEAFALHEAL 317 Query: 318 FPH-KVERLDPVVRDRVRWAEQVSSVEYLR---RKAVLQRCGAGAARLFDDVD--VLLTP 371 ERLDP VR R+ A +++ + L+ ++ LQR +L +++D VL+TP Sbjct: 318 LDSADAERLDPRVRRRLEAARPMTASQVLKLYDARSTLQR------QLVEELDGAVLITP 371 Query: 372 TVPASPPRLADI-GTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMG 430 TV P LA + E +A N+ + T +L + +P G D+ +P GL L Sbjct: 372 TVAHVAPPLAPLEADDELFARTNLATLSLTMPGSLLDMPGVNLPSGRDSQGLPTGLLLSV 431 Query: 431 PPRAEARLIGIALGIEALI 449 P +ARL+ +A +EA++ Sbjct: 432 PQGEDARLLRVARSVEAML 450 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: 475 Number of extensions: 26 Number of successful extensions: 5 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: 453 Length adjustment: 33 Effective length of query: 429 Effective length of database: 420 Effective search space: 180180 Effective search space used: 180180 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