Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 361 bits (927), Expect = e-104 Identities = 200/480 (41%), Positives = 278/480 (57%), Gaps = 12/480 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI GKFVP + G+ F+NI+P VA A +++LA+ AA A W K + E Sbjct: 21 NFIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKS-WGKTSPTE 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ D + E L+ E+LD GKP + + DIP A +F +F+ +RT Sbjct: 80 RANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGSI 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +D+ Y P+GV+G I PWN P+L+ WKLAPALAAGN VV+KPAE TP + V Sbjct: 140 CPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L E+ D +P GVVN+V GFG AG L + + I+FTGETTTG++IM A++ L Sbjct: 200 LIELIADL-IPPGVVNIVQGFGV-EAGKPLASNKRIAKIAFTGETTTGRLIMQYASQNLI 257 Query: 253 RLSYELGGKNPNVIFAD--SNLDEVIETTMKS---SFINQGEVCLCGSRIYVERPAYEAF 307 ++ ELGGK+PN+ FAD D+ + ++ +NQGEVC C SR+ V+ YE F Sbjct: 258 PVTLELGGKSPNIFFADVLDKDDDFFDKALEGFAMFALNQGEVCTCPSRVLVQESIYERF 317 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--- 364 +E+ + + + G+P D T +GA S E E++ YI + +EG +L GG R E Sbjct: 318 IERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGREELGG 377 Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424 L GY+++PT+ G R+ +EEIFGPVV+V F EEE L NDT YGL A +WT Sbjct: 378 DLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAGLWT 436 Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 D RA R+ +I+AG VW N + L FGG KQSGIGRE + Y + N+ + Sbjct: 437 RDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLV 496 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: 591 Number of extensions: 35 Number of successful extensions: 7 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 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