Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Cola:Echvi_1497 Length = 469 Score = 155 bits (391), Expect = 4e-42 Identities = 102/340 (30%), Positives = 171/340 (50%), Gaps = 11/340 (3%) Query: 142 YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAG 201 Y P G + +I+PWN P L L A+AAG + +KP+E +P T+ +L + + Sbjct: 97 YLQAEPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEHSPHTSALLRRMVTELF 156 Query: 202 VPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGK 261 + V G S L E P + I FTG T GKI+M +AAK L ++ ELGGK Sbjct: 157 AVEDVTIFEGGVPVTSE---LLEQP-FDHIFFTGSTEVGKIVMKAAAKNLTSVTLELGGK 212 Query: 262 NPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKEL--V 319 +P +I +L++ + FIN G+ C+ ++V + F+E A+ + Sbjct: 213 SPAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQDFIETLKAQVNRMYNA 272 Query: 320 VGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITG 379 G FD G +I H R+ +K A +G + GGK L++ F+EPT+++ Sbjct: 273 NGKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGK--NSLDQ-QFMEPTVVSN 329 Query: 380 LTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEA 439 ++ ++KEEIFGP++ +I + ++V++ I L+ +T D R +++ + Sbjct: 330 VSEAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFTTDDRIIEQLSKNTSS 389 Query: 440 GIVWVNTWFLRDLRT--PFGGMKQSGIGREGGLHSFEFYS 477 G + +N ++ L + PFGG+ SG+GR G F +S Sbjct: 390 GALVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFS 429 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: 521 Number of extensions: 28 Number of successful extensions: 6 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: 469 Length adjustment: 34 Effective length of query: 452 Effective length of database: 435 Effective search space: 196620 Effective search space used: 196620 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