Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 299 bits (765), Expect = 2e-85 Identities = 173/468 (36%), Positives = 264/468 (56%), Gaps = 9/468 (1%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H+I G++V S G D INPATE + + G A+ D AV AAK A + + + + +E Sbjct: 7 HYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDS-FSRTSVDE 65 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 RIA+L + R +L+ + + G P L+ + + + + ++ Sbjct: 66 RIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKAFEFS- 124 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 + + + + P+GV+ LI PWN PL + K+APALAAGNT+V+KP+E P +A + Sbjct: 125 ---EQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAI 181 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 AEI AGVP GV NLV G GP G AL+ H DV+ +SFTG T G + +AA+T+K Sbjct: 182 FAEIMDKAGVPAGVFNLVQGDGP-IVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETVK 240 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 R+ ELGGK+PNVI ++L ++ + S +N G+ C+ +R+ V + Sbjct: 241 RVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIAS 300 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK-RPEGLEKGYF 371 K + GDP +G +++ +E++ G I+ +EEG + TGG RP+G+E GYF Sbjct: 301 GLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIETGYF 360 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 ++PT+ +G+ D + +EEIFGPV+T+IP+ EEE + NDT YGLSA ++ + Sbjct: 361 VKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSP-EEVK 419 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSEL 479 RVA ++ AG+V++N D PFGG KQSG GRE G + E+ Sbjct: 420 RVAPRLRAGMVYINGG-QPDPSLPFGGYKQSGNGREHGKFGLAEFMEV 466 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: 556 Number of extensions: 29 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: 474 Length adjustment: 34 Effective length of query: 452 Effective length of database: 440 Effective search space: 198880 Effective search space used: 198880 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: 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