Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 315 bits (808), Expect = 2e-90 Identities = 181/483 (37%), Positives = 282/483 (58%), Gaps = 9/483 (1%) Query: 8 PIDCLHFIDGKFVPSLDGKTFDNINPATEEKL-GTVAEGGAAEIDLAVQAAKKALNGPWK 66 P++C ++I+G+++ + T ++ NPA + ++ T A + D AV AA++A G W+ Sbjct: 4 PLNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAY-GSWR 62 Query: 67 KMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIR 126 K+ A R + +VG+L+L+ KEEL+ L S + GKP + D+ + + R Sbjct: 63 KVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGR 121 Query: 127 TITNEATQMD-DVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAEL 185 + + T + +R P+GV LI PWN P+ + WK PAL GNTV++KPAE Sbjct: 122 RLFGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAED 181 Query: 186 TPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA 245 TP AT L EI AG+P GV+NLVHG G AG AL EHP+++ +SFTG + TG + Sbjct: 182 TPACATKLIEIFAAAGLPPGVINLVHGVG-EEAGKALVEHPNIDLVSFTGSSATGAYVGE 240 Query: 246 SAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYE 305 + +T KR+ E+GGKN V+ D++L+ ++ + +F G+ C SR+ + R E Sbjct: 241 TCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKE 300 Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK-RPE 364 F +T +L +G + +T +G +I++ +RV Y+ +A EEG IL GG+ E Sbjct: 301 KFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTE 360 Query: 365 G-LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 G L++GYF +PTI+ +T RV +EEIFGPVV +I T EE + +NDT YGLS+SV+ Sbjct: 361 GQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVY 420 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFL-RDLRTPFGGMKQSGIG-REGGLHSFEFYSELTN 481 T D+ RA IE GI ++N + ++ PFGG+KQ+G G RE G + + ++E + Sbjct: 421 TRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKS 480 Query: 482 ICI 484 + + Sbjct: 481 VYV 483 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: 585 Number of extensions: 27 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: 498 Length adjustment: 34 Effective length of query: 452 Effective length of database: 464 Effective search space: 209728 Effective search space used: 209728 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