Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate GFF3601 HP15_3543 amidase signature enzyme
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Marino:GFF3601 Length = 470 Score = 142 bits (358), Expect = 2e-38 Identities = 120/397 (30%), Positives = 183/397 (46%), Gaps = 21/397 (5%) Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGS---DEALPEAWQAAGPLVARLQRQLGIVVGKT 122 + G L G+P VKDL V G GS A P A V RL Q + GKT Sbjct: 73 EQFGLLDGIPFGVKDLIDVEGCTTSRGSLLYRNAPPAKRNAEA--VERLGFQGMVFGGKT 130 Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182 + E AF G+G N +G+P NP + + GGSS+G+ + G ++LGTDT+GS R Sbjct: 131 NLSELAFSGVGTNDLFGSPINPRATTGKYITGGSSSGSAAGVASGLWPVSLGTDTSGSSR 190 Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP 242 +PA+ G VG K + R+P+ G+ PL+ SLD G+ TV+D LD +GL AP Sbjct: 191 IPAAFCGVVGFKPSFDRYPLRGVAPLAPSLDHLGINALTVQDC----VILDQALRGL-AP 245 Query: 243 AP---VRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQV--VRF-PLPHCEEA 296 P + + VP N DP I + + L+ G ++ V F P + Sbjct: 246 IPKFRMLSEQTEFLVPRNKSIQPRDPHIKDNFDKTLDLLSNLGFEIHEVDFSPYAEVDRL 305 Query: 297 FDIFRRGGLAASELAAYLDQHFPHKV-ERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCG 355 F+I G L A E A + F + + +DP + R++ ++ Y + + + Sbjct: 306 FEI--HGSLVAHEAAQQYEALFENGLTSYIDPKILQRLKEGTLLNRKSYALLQKIRRNLR 363 Query: 356 AGAARLFDDVDVLLTPTVPASPPRLADI-GTVETYAPANMKAMRNTAISNLFGWCALTMP 414 A + + +LL PTV PP + + VE + N + NT +N G A+ +P Sbjct: 364 AELSSSIGN-KILLQPTVKILPPAIESVLKGVEEFKAFNKLILGNTMYANYLGMPAIAIP 422 Query: 415 VGLDANRMPVGLQLMGPPRAEARLIGIALGIEALIGQ 451 +G N +QL + L+ AL +EA + + Sbjct: 423 IGHAPNGFSTSIQLSAASGKDDFLLKTALFLEAALSK 459 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: 416 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: 470 Length adjustment: 33 Effective length of query: 429 Effective length of database: 437 Effective search space: 187473 Effective search space used: 187473 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