Align Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_028950880.1 Q385_RS0106445 aldehyde dehydrogenase
Query= SwissProt::Q92UV7 (485 letters) >NCBI__GCF_000619805.1:WP_028950880.1 Length = 474 Score = 297 bits (760), Expect = 6e-85 Identities = 170/467 (36%), Positives = 266/467 (56%), Gaps = 9/467 (1%) Query: 15 MRIAGRLVDTDDRVEVRYPWNDTVVGTVPAGRAEHAREAFAIAAAYQPKL---TRYERQK 71 M I G+ V D+ ++V YP+N +G G E +A A KL T YE+ K Sbjct: 6 MLIGGKEVFKDEVIDVIYPYNQQKIGEAVKGSVEDVEKAVEKAKIGLKKLKQLTAYEKYK 65 Query: 72 ILLATAEALAARKEEISDVITLELGISKADSLYEVGRAFDVFTLAGQMCIRDDGEIFSCD 131 +LL A+ L RKEE + VITLE G + +S EV RA + T + + R GE+ D Sbjct: 66 MLLKVAQLLEERKEEFAKVITLETGKTIKESRIEVDRAINTITFSAEEAKRIAGEVVHFD 125 Query: 132 LTPHGKARKIFTMREPLTAISAITPFNHPLNMVAHKVAPAIATNNCVVVKPTELTPMTAL 191 +P+G+ ++ + R P ++AITPFN P+N+ AHK+APAIA ++KP+E TP++ Sbjct: 126 ASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEKTPLSPT 185 Query: 192 LLADILYEAGLPPEMLSVVTGWPADIGMEMITNPHVDLVTFTGSVPVGKLIAANAHYKRQ 251 +L + EAG+P E +S++ G+ AD+G M T+ V +V+FTGS+ VG++IA A K+ Sbjct: 186 MLCQLFLEAGVPEEAVSIIPGF-ADVGQAMTTHSDVRVVSFTGSLKVGEIIAKQAGLKKI 244 Query: 252 VLELGGNDPLIILNDLSDDDLARAADLAVAGATKNSGQRCTAVKRILCQESVADRFVPLV 311 V+ELG N +I+ D +L AA +V G +GQ C +V+R+L + VAD F L+ Sbjct: 245 VMELGSNSAVIVDKDA---NLELAAKKSVLGGFALAGQVCISVQRVLVHKDVADEFENLL 301 Query: 312 LERAKRLRFGDPMDRSTDLGTVIHEKAAALFEERVMRAAEEGADILYHPGRSGALLPPIV 371 + A +L++GDPM+ TD+G VI + + A +GA + LL P + Sbjct: 302 KKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGGEAEKTLLKPTI 361 Query: 372 VDRVPHQSDLVLEETFGPIIPIVRVPDDDDATITLSNSTAFGLSSGVCTNDYRRMQKYIA 431 V +P S L EE F P++ + R ++A + + N T +GL G+ TN+ + K I Sbjct: 362 VSEIPEDSKLFYEEAFAPVVAVKRFETIEEA-VEMVNKTNYGLQVGIFTNNLKNAWKVIE 420 Query: 432 GLKVGTVNIWEVPGYRIEMSPFGGIKDSGNGYKEGVIEAMKSFTNVK 478 ++VG V + ++P +R + P+GG+K SG G +EG A++ +T +K Sbjct: 421 EVEVGGVMVNDIPTFRADNMPYGGVKGSGIG-REGPKFAIEDYTEIK 466 Lambda K H 0.320 0.136 0.399 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: 450 Number of extensions: 21 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: 485 Length of database: 474 Length adjustment: 34 Effective length of query: 451 Effective length of database: 440 Effective search space: 198440 Effective search space used: 198440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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