Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate Pf6N2E2_3707 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3707 Length = 457 Score = 193 bits (490), Expect = 1e-53 Identities = 146/413 (35%), Positives = 217/413 (52%), Gaps = 21/413 (5%) Query: 49 ARARSAAAAVDTLLDQGQDLGPLMGLPVSVKDLYGVPGLPVFAGSD---EALPEAWQAAG 105 ARAR A A GQ L G+P++ KDL+ V G A + +A P AA Sbjct: 51 ARARREAQASAARWRAGQPLSGFDGVPLAWKDLFDVAGSVTTAAAAVRRDAPPALLDAAS 110 Query: 106 PLVARLQRQLGIVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLV 165 V+ L R + +GKT+ EFA+ GLG+N H+GTP NP+S + R+PGGSS+G+ V++ Sbjct: 111 --VSLLSRAGMVCLGKTNLSEFAYSGLGLNPHFGTPVNPFSDAQPRIPGGSSSGSAVAVA 168 Query: 166 QGSALLALGTDTAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDL 225 G +A+GTDTAGS+RVPA+ VG + + R +G+ PL+ S+D+ G LTR+V D Sbjct: 169 AGIVPIAMGTDTAGSIRVPAAFNALVGFRASSRRHSRDGVFPLAHSIDSIGPLTRSVRD- 227 Query: 226 AYAFAALDTESQGLPAPAPVRVQGLRVGVPTNHFWD-DIDPSIAAAVEAAVQRLAQAGAQ 284 A+ L AP + G R V D ++ ++ A V A VQ L AGA Sbjct: 228 AWMIDELLQGRDPRQAPPVRSLAGQRFWVEQAVLEDASVEAAVRANVLAGVQALRTAGAL 287 Query: 285 VVRFPLPHCEEAFDIFR-RGGLAASELAAYLDQHFPH-KVERLDPVVRDRVRWAEQVSSV 342 V PLP + + + R G L A+E A + ERLDP VR R+ A +++ Sbjct: 288 VEIRPLPAFQASLALIRDHGWLGAAEAFALHEALLDSADAERLDPRVRRRLEAARPMTAS 347 Query: 343 EYLR---RKAVLQRCGAGAARLFDDVD--VLLTPTVPASPPRLADI-GTVETYAPANMKA 396 + L+ ++ LQR +L +++D VL+TPTV P LA + E + N+ Sbjct: 348 QVLKLYDARSALQR------QLVEELDGAVLITPTVAHVAPPLAPLEADDELFVRTNLAT 401 Query: 397 MRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALI 449 +R T +L ++ +P G D+ +P GL L P +ARL+ +A +EA + Sbjct: 402 LRLTMPGSLLDMPSVNLPSGRDSQGLPTGLLLSVPQGEDARLLRVARSVEATL 454 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: 481 Number of extensions: 24 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: 457 Length adjustment: 33 Effective length of query: 429 Effective length of database: 424 Effective search space: 181896 Effective search space used: 181896 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