Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_012757049.1 RLEG_RS07320 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000023185.1:WP_012757049.1 Length = 506 Score = 350 bits (898), Expect = e-101 Identities = 191/479 (39%), Positives = 283/479 (59%), Gaps = 16/479 (3%) Query: 7 KPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPW 65 K D IDG++ + + P+ + G + + A+ AA+KA + GPW Sbjct: 14 KARDFKMLIDGRWEAGASDP-IERVAPSHGVVVSRFPTGSRKDAERAISAARKAFDLGPW 72 Query: 66 KKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTW-----LSGSIDIPRAAYNFHF 120 +MTA+ER A+L K DLI R EEL+ L++++ GKP ++GS+DI R A Sbjct: 73 PRMTASERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYA----- 127 Query: 121 FSDYIRTITNEA-TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVV 179 + R + E+ + D L +R +GV+ +I PWN P L++ KL ALAAG T V Sbjct: 128 -AALARDLHGESYNTLGDGTLGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTV 186 Query: 180 MKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTT 239 +KP+ELT + VL EI + AG+PDGVVN+V G GP GA +T HPDV+ +SFTG T Sbjct: 187 VKPSELTSGSTLVLGEILQQAGIPDGVVNIVTGTGPE-VGAIMTSHPDVDMVSFTGSTGV 245 Query: 240 GKIIMASAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYV 299 GK+ M++AA+TLK++S ELGGKNP ++F D++L I+ + ++ N GE C GSR+ + Sbjct: 246 GKLTMSNAAQTLKKVSLELGGKNPQIVFPDADLGAFIDAAVFGAYFNAGECCNAGSRLIL 305 Query: 300 ERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTG 359 + +++ +K + VGDP D T+VGA+I+ +H E+++GY+ A G + G Sbjct: 306 HKSIASDVVKRIAELSKAVKVGDPLDPSTQVGAIITPQHLEKISGYVAGARSSGARVAHG 365 Query: 360 GKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLS 419 G+ + L G F+ PTI+ +T D V +EE+FGPV++V+ F+T E + N YGLS Sbjct: 366 GETLD-LGMGQFMSPTILEEVTPDMAVAREEVFGPVLSVLTFETSAEAIRIANSIDYGLS 424 Query: 420 ASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 A VW+ D + + AG VW+NT+ PFGG KQSG+GRE G H+ E Y+E Sbjct: 425 AGVWSRDFDTCLTIGRSVRAGTVWMNTFMDGASELPFGGYKQSGLGRELGRHAVEDYTE 483 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: 681 Number of extensions: 33 Number of successful extensions: 4 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: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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 Apr 09 2024. 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