Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_053938969.1 WG78_RS16670 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_001294205.1:WP_053938969.1 Length = 466 Score = 665 bits (1716), Expect = 0.0 Identities = 324/466 (69%), Positives = 391/466 (83%), Gaps = 2/466 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 MQLKD+ L RQQ F++GAW+DADN +T+ VNNPATGEI+ +PK+G AETRRAIEAA A Sbjct: 1 MQLKDSSLLRQQCFVNGAWIDADNQETVPVNNPATGEIIAHIPKLGKAETRRAIEAAQAA 60 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 PAWR+ TAKER+ LR+W +L++ N DDL ++T EQGKPLAEA+GEI YAAS+IEWFA Sbjct: 61 WPAWRSKTAKERSQILRKWNDLMLANVDDLALILTSEQGKPLAEARGEITYAASYIEWFA 120 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EEA+RI GD+I D+R++V+KQPIGVTAAITPWNFPAAMITRK GPALAAGC MV+K Sbjct: 121 EEARRIEGDIIAPPSNDRRILVLKQPIGVTAAITPWNFPAAMITRKVGPALAAGCPMVLK 180 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240 PA+QTP SALAL LA RAG+P G+ +V+TGS+ +IGGELT++PIVRK++FTGSTE+G + Sbjct: 181 PATQTPLSALALAVLAERAGVPAGIFNVLTGSSTEIGGELTASPIVRKITFTGSTEVGAK 240 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 L+ + A IKK+S+ELGGNAPFIVFDDADLD AV+GAI SKYRN+GQTCVCANRL +Q Sbjct: 241 LIEQSAPTIKKMSMELGGNAPFIVFDDADLDAAVQGAIGSKYRNSGQTCVCANRLLVQAG 300 Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359 VYDAFA+KL AV LK+GNG+++G T GPLID+KA+AK++EHIADA KGA +L GGK Sbjct: 301 VYDAFAQKLADAVNALKVGNGVDDGVTQGPLIDDKAIAKIEEHIADATGKGAQVLTGGKR 360 Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 ++ G FFEPTIL V VA+EETFGPLAPLF+F+ E E IAM+NDTEFGLASYFY Sbjct: 361 HALGGTFFEPTILTGVTPAMKVAREETFGPLAPLFKFETEEEAIAMANDTEFGLASYFYT 420 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSK 464 RDL R+FRVAE LEYGMVG+N GLIS+EVAPFGG+K SGLGREGS+ Sbjct: 421 RDLARIFRVAEGLEYGMVGINAGLISSEVAPFGGVKQSGLGREGSR 466 Lambda K H 0.317 0.135 0.390 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: 697 Number of extensions: 13 Number of successful extensions: 2 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: 480 Length of database: 466 Length adjustment: 33 Effective length of query: 447 Effective length of database: 433 Effective search space: 193551 Effective search space used: 193551 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: 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