Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 305 bits (780), Expect = 3e-87 Identities = 171/466 (36%), Positives = 267/466 (57%), Gaps = 9/466 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +IDG +V T D INPATEE G ++ G A++D AV+AA+KA + + + ER Sbjct: 8 YIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAF-ASFSQTSREER 66 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 I +L ++ +R E+++ + + G P WL+ + + ++ E Sbjct: 67 IDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQTAAAVLKGYKFE-- 124 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 +D ++ P+GV I PWN P+ + K+ PA+A G T+V+KP+E+ P + + Sbjct: 125 --EDRGTTRIVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPSEIAPFSGYIW 182 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253 EI AGVP GV NLV+G GP + GAAL+ HP+V+ +SFTG T G + +AA T+KR Sbjct: 183 TEIMHAAGVPAGVFNLVNGDGP-TVGAALSRHPEVDMVSFTGSTRAGIEVAKNAAPTVKR 241 Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313 + ELGGK+PN+I D++ + + S +N G+ C +R+ V + + A Sbjct: 242 VHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARMDEVIAIAKA 301 Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK-RPEGLEKGYFL 372 + VGDP + K+G ++S+ + ++ G I+ ++EG T++TGG RPEGL+KGY++ Sbjct: 302 AAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRPEGLDKGYYV 360 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 +PT+ +T + + KEEIFGPVV+++ +DT +E + NDT YGL+A V D + Sbjct: 361 KPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVSGGDQDEVRK 420 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 VA ++ AG V +N DL PFGG K SG GRE G H+F + E Sbjct: 421 VASRLRAGQVTLN-GAGPDLMAPFGGYKMSGNGREWGDHAFGEFLE 465 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: 579 Number of extensions: 33 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: 479 Length adjustment: 34 Effective length of query: 452 Effective length of database: 445 Effective search space: 201140 Effective search space used: 201140 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