Align Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate SM_b21539 SM_b21539 aldehyde dehydrogenase
Query= SwissProt::Q92UV7 (485 letters) >FitnessBrowser__Smeli:SM_b21539 Length = 485 Score = 963 bits (2490), Expect = 0.0 Identities = 485/485 (100%), Positives = 485/485 (100%) Query: 1 MTNAEVTIAVRHEPMRIAGRLVDTDDRVEVRYPWNDTVVGTVPAGRAEHAREAFAIAAAY 60 MTNAEVTIAVRHEPMRIAGRLVDTDDRVEVRYPWNDTVVGTVPAGRAEHAREAFAIAAAY Sbjct: 1 MTNAEVTIAVRHEPMRIAGRLVDTDDRVEVRYPWNDTVVGTVPAGRAEHAREAFAIAAAY 60 Query: 61 QPKLTRYERQKILLATAEALAARKEEISDVITLELGISKADSLYEVGRAFDVFTLAGQMC 120 QPKLTRYERQKILLATAEALAARKEEISDVITLELGISKADSLYEVGRAFDVFTLAGQMC Sbjct: 61 QPKLTRYERQKILLATAEALAARKEEISDVITLELGISKADSLYEVGRAFDVFTLAGQMC 120 Query: 121 IRDDGEIFSCDLTPHGKARKIFTMREPLTAISAITPFNHPLNMVAHKVAPAIATNNCVVV 180 IRDDGEIFSCDLTPHGKARKIFTMREPLTAISAITPFNHPLNMVAHKVAPAIATNNCVVV Sbjct: 121 IRDDGEIFSCDLTPHGKARKIFTMREPLTAISAITPFNHPLNMVAHKVAPAIATNNCVVV 180 Query: 181 KPTELTPMTALLLADILYEAGLPPEMLSVVTGWPADIGMEMITNPHVDLVTFTGSVPVGK 240 KPTELTPMTALLLADILYEAGLPPEMLSVVTGWPADIGMEMITNPHVDLVTFTGSVPVGK Sbjct: 181 KPTELTPMTALLLADILYEAGLPPEMLSVVTGWPADIGMEMITNPHVDLVTFTGSVPVGK 240 Query: 241 LIAANAHYKRQVLELGGNDPLIILNDLSDDDLARAADLAVAGATKNSGQRCTAVKRILCQ 300 LIAANAHYKRQVLELGGNDPLIILNDLSDDDLARAADLAVAGATKNSGQRCTAVKRILCQ Sbjct: 241 LIAANAHYKRQVLELGGNDPLIILNDLSDDDLARAADLAVAGATKNSGQRCTAVKRILCQ 300 Query: 301 ESVADRFVPLVLERAKRLRFGDPMDRSTDLGTVIHEKAAALFEERVMRAAEEGADILYHP 360 ESVADRFVPLVLERAKRLRFGDPMDRSTDLGTVIHEKAAALFEERVMRAAEEGADILYHP Sbjct: 301 ESVADRFVPLVLERAKRLRFGDPMDRSTDLGTVIHEKAAALFEERVMRAAEEGADILYHP 360 Query: 361 GRSGALLPPIVVDRVPHQSDLVLEETFGPIIPIVRVPDDDDATITLSNSTAFGLSSGVCT 420 GRSGALLPPIVVDRVPHQSDLVLEETFGPIIPIVRVPDDDDATITLSNSTAFGLSSGVCT Sbjct: 361 GRSGALLPPIVVDRVPHQSDLVLEETFGPIIPIVRVPDDDDATITLSNSTAFGLSSGVCT 420 Query: 421 NDYRRMQKYIAGLKVGTVNIWEVPGYRIEMSPFGGIKDSGNGYKEGVIEAMKSFTNVKTF 480 NDYRRMQKYIAGLKVGTVNIWEVPGYRIEMSPFGGIKDSGNGYKEGVIEAMKSFTNVKTF Sbjct: 421 NDYRRMQKYIAGLKVGTVNIWEVPGYRIEMSPFGGIKDSGNGYKEGVIEAMKSFTNVKTF 480 Query: 481 SLPWP 485 SLPWP Sbjct: 481 SLPWP 485 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: 891 Number of extensions: 29 Number of successful extensions: 1 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: 485 Length adjustment: 34 Effective length of query: 451 Effective length of database: 451 Effective search space: 203401 Effective search space used: 203401 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: 52 (24.6 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