Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO356_25765 AO356_25765 carnitine dehydratase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25765 Length = 493 Score = 359 bits (922), Expect = e-103 Identities = 190/474 (40%), Positives = 284/474 (59%), Gaps = 4/474 (0%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGP-WKKMTANER 73 I G++V +L GKTF+++NPA + + + A+++ AVQAA+ A + P W+ +TA R Sbjct: 10 IGGEWVDALSGKTFESLNPALAQPWAELPDADEADVERAVQAAQSAFDSPAWRGLTATAR 69 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 +LR++GDLI E KE+L+ LES D GK + + FH+ + + Sbjct: 70 GKLLRRLGDLIAENKEQLAQLESRDNGKLIRETRG-QVGYLPEFFHYTAGLADKLEGGTL 128 Query: 134 QMDDVAL-NYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +D L Y + +GV+ I PWN PL L KLAPALAAGNT+V+KP+E T Sbjct: 129 PLDKPDLFAYTVHEAMGVVAAIIPWNSPLYLTAIKLAPALAAGNTIVIKPSEHASATVLE 188 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 LA + +AG+P GVVN+V G+GP S GAALT HP V I+FTG T + ++ S+A+ Sbjct: 189 LARLALEAGIPPGVVNVVTGYGP-STGAALTRHPLVRKIAFTGGAATARHVVRSSAENFA 247 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 +LS ELGGK+PN+IFAD++LD I + + G+ C+ GSR+ V+ Y+ F+ + V Sbjct: 248 KLSLELGGKSPNIIFADADLDSAINGAIAGIYAASGQSCVSGSRLLVQDEIYDEFVSRLV 307 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372 + + + +G+P + +++G + + + V G + A+ EG + GGKRP+ L G+F Sbjct: 308 ERAQRIRIGNPQEDASEMGPMATAQQLAVVEGLVADAIAEGARLRLGGKRPQNLGDGWFY 367 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 EPT+ ++++EE+FGPV +VI F E E L ND+ +GL+A +WT DL RAHR Sbjct: 368 EPTLFECDRNSMKIMQEEVFGPVASVIRFKDEAEALAIANDSQFGLAAGIWTRDLGRAHR 427 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 +A + +GI+WVNT+ P GG K SG GRE G+ S Y+EL + I L Sbjct: 428 LARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKTVWINL 481 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: 615 Number of extensions: 17 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: 493 Length adjustment: 34 Effective length of query: 452 Effective length of database: 459 Effective search space: 207468 Effective search space used: 207468 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