Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001592305.1:WP_068168204.1 Length = 485 Score = 363 bits (933), Expect = e-105 Identities = 198/483 (40%), Positives = 289/483 (59%), Gaps = 8/483 (1%) Query: 6 VKPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPW 65 + P FI+G+ V G+ F+++NPAT V E +++ AV+AA W Sbjct: 1 MNPTTLFSFINGQTVNG-GGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGF-ALW 58 Query: 66 KKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYI 125 M+A ER +LR+ D++ ER EL+ LE D GKP + +D+ A +F+ Sbjct: 59 SAMSATERGRILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAA 118 Query: 126 RTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAEL 185 T+T + + + A Y + P+GV I WN P+ + WK APALAAGN ++ KP+EL Sbjct: 119 ATLTGQQYPLKN-AFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEL 177 Query: 186 TPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA 245 TP TA LAE+ +AGVP GV N+V G G + GA L HPDV +S TG TGK +M Sbjct: 178 TPATAVKLAEVYLEAGVPPGVFNVVQGRG--AVGAMLAAHPDVAKVSVTGSVPTGKRVME 235 Query: 246 SAAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYE 305 +AA TLKR++ ELGGK+P ++F D++L++ + M +F QGEVC +R++V+R Sbjct: 236 TAAGTLKRVTMELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAP 295 Query: 306 AFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR--P 363 FL + +T L VGDP D T++GALIS+ H RV YI EG T++ GG+R Sbjct: 296 RFLARLKERTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAV 355 Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 EGL F+ PTI D R+V+EEIFGPV++++ FDTE E + + N + + L+A V+ Sbjct: 356 EGL-GDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVF 414 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 T DL+R HRVA QI AGI W+N + + + PFGG+ +SGIG E + + + Y++L + Sbjct: 415 TTDLQRGHRVAAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVY 474 Query: 484 IKL 486 ++L Sbjct: 475 VEL 477 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: 555 Number of extensions: 22 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: 485 Length adjustment: 34 Effective length of query: 452 Effective length of database: 451 Effective search space: 203852 Effective search space used: 203852 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