Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Smeli:SMc04397 Length = 504 Score = 358 bits (920), Expect = e-103 Identities = 189/471 (40%), Positives = 288/471 (61%), Gaps = 15/471 (3%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANER 73 IDG++V +G+T + + P + A+ + A+ AA++A + GPW +MTA+ER Sbjct: 24 IDGQWVDGAEGRTIERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPRMTASER 83 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTW-----LSGSIDIPRAAYNFHFFSDYIRTI 128 +L + D+I R +EL+ L+++++GKP L+G+ DI R A + R + Sbjct: 84 SLILLRAADMIAARADELAFLDAVESGKPISQAKGELAGAADIWRYA------AALAREL 137 Query: 129 TNEA-TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187 + E+ + + L +R P+GV+ +I PWN P L+++ KL ALAAG T V+KP+ELT Sbjct: 138 SGESYNTLGEGTLGVVLREPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTS 197 Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247 + VL EI AGVP GVVN++ G GP AGA LT HP V+ +SFTG T G++ MA+A Sbjct: 198 ASTLVLGEILEAAGVPQGVVNIIVGTGPE-AGAPLTTHPHVDMVSFTGSTGIGQLTMANA 256 Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307 A+TLK++S ELGGKNP ++F D+NLDE I+ + ++ N GE C GSR+ + R E Sbjct: 257 AQTLKKVSLELGGKNPQIVFPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRDIAEEV 316 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLE 367 + + + ++ VGDP D +T+VGA+I+ +H +++ GY+ A EG I GG + L Sbjct: 317 TARIASLSAKVKVGDPLDPETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTTLD-LG 375 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 G F+ PTI++ + + V +EE+FGPV++V+ F+ EE + N YGLSA VW+ D Sbjct: 376 MGQFMAPTILSAVRPEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVWSRDF 435 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 + ++ AG VW+NT+ PFGG +QSG+GRE G H+ E Y+E Sbjct: 436 DTCLTIGRRVRAGTVWMNTFMDGASELPFGGYRQSGLGRELGRHAVEDYTE 486 Lambda K H 0.318 0.136 0.404 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: 637 Number of extensions: 28 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: 486 Length of database: 504 Length adjustment: 34 Effective length of query: 452 Effective length of database: 470 Effective search space: 212440 Effective search space used: 212440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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