Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 276 bits (706), Expect = 1e-78 Identities = 167/473 (35%), Positives = 243/473 (51%), Gaps = 21/473 (4%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 +DGK P +TF I+PAT A++D AV AA++A G W +R Sbjct: 8 VDGK--PLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPG-WAATPIEDRA 64 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPT-----WLSGSIDIPRAAYNFHFFSDYIRTIT 129 A + + D I K+EL+ L S + GKP + G++ RA D ++ Sbjct: 65 AAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKD-- 122 Query: 130 NEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMT 189 DD R+P+GV+ I+PWN P+++ W + P L AGNTVVMKP+ TP+ Sbjct: 123 ------DDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLA 176 Query: 190 ATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAK 249 A + EI +A +P GV+N V G G A+ HP ++ I FTG T TG+ IMA A Sbjct: 177 ALRMVEIA-NAHLPPGVLNSVTG--EVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAA 233 Query: 250 TLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLE 309 LKRL+ ELGG + ++ D+++D+V +F N G++C R+YV ++A E Sbjct: 234 NLKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAE 293 Query: 310 KFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKG 369 K + VVG DA ++ G + + + ++ V A GG L GG+ EG G Sbjct: 294 KLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREG--DG 351 Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429 YF +++ +T R+V EE FGP++ VI + E+ L + N GL SVW+ D Sbjct: 352 YFFPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAA 411 Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 A A ++EAG VWVN PFGG KQSG+G E GL+ E Y +L + Sbjct: 412 ALAFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTV 464 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: 533 Number of extensions: 33 Number of successful extensions: 5 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