Align Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_012674904.1 SULAZ_RS00135 aldehyde dehydrogenase
Query= SwissProt::Q92UV7 (485 letters) >NCBI__GCF_000021545.1:WP_012674904.1 Length = 474 Score = 302 bits (773), Expect = 2e-86 Identities = 174/468 (37%), Positives = 266/468 (56%), Gaps = 9/468 (1%) Query: 14 PMRIAGRLVDTDDRVEVRYPWNDTVVGTVPAGRAEHAREAFAIAAAYQPKL---TRYERQ 70 PM I G V D+ ++V YP+N VG G E +A A KL T YE+ Sbjct: 5 PMLIGGEEVFKDEVIDVIYPYNQQKVGEAVKGSVEDVEKAVEKAKVGLKKLKQLTAYEKY 64 Query: 71 KILLATAEALAARKEEISDVITLELGISKADSLYEVGRAFDVFTLAGQMCIRDDGEIFSC 130 KILL A+ L RK+E + VITLE G + +S EV RA + T + + R GE+ Sbjct: 65 KILLKVAQLLEERKDEFAKVITLETGKTIKESRVEVERAINTITFSAEEAKRIGGEVVHF 124 Query: 131 DLTPHGKARKIFTMREPLTAISAITPFNHPLNMVAHKVAPAIATNNCVVVKPTELTPMTA 190 D +P+G+ ++ + R P ++AITPFN P+N+ AHK+APAIA ++KP+E TP++ Sbjct: 125 DASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEKTPLSP 184 Query: 191 LLLADILYEAGLPPEMLSVVTGWPADIGMEMITNPHVDLVTFTGSVPVGKLIAANAHYKR 250 +L + EAG+P E +S++ G+ AD+G M T+P V +V+FTGS+ VG++IA A K+ Sbjct: 185 TMLCQLFLEAGVPKEAVSIIPGF-ADVGQAMTTHPDVRVVSFTGSLKVGEIIAKQAGLKK 243 Query: 251 QVLELGGNDPLIILNDLSDDDLARAADLAVAGATKNSGQRCTAVKRILCQESVADRFVPL 310 V+ELG N +I+ D +L AA +V G +GQ C +V+R+L + VAD F L Sbjct: 244 IVMELGSNSAVIVDKDA---NLELAAKKSVLGGFALAGQVCISVQRVLVHKEVADEFENL 300 Query: 311 VLERAKRLRFGDPMDRSTDLGTVIHEKAAALFEERVMRAAEEGADILYHPGRSGALLPPI 370 + + A +L++GDPM+ TD+G VI + + A +GA + L P Sbjct: 301 LKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGGQAEKTLFKPT 360 Query: 371 VVDRVPHQSDLVLEETFGPIIPIVRVPDDDDATITLSNSTAFGLSSGVCTNDYRRMQKYI 430 +V VP S L EE F P++ + R ++A I + N T +GL G+ TN+ + K I Sbjct: 361 IVSEVPEDSKLFYEEAFAPVVAVKRFETIEEA-IEMVNKTNYGLQVGIFTNNLKNAWKVI 419 Query: 431 AGLKVGTVNIWEVPGYRIEMSPFGGIKDSGNGYKEGVIEAMKSFTNVK 478 ++VG V + ++P +R + P+GG+K SG G +EG A++ +T +K Sbjct: 420 EEVEVGGVMVNDIPTFRADNMPYGGVKGSGIG-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: 472 Number of extensions: 23 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