Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_022948198.1 H035_RS0106590 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_000421465.1:WP_022948198.1 Length = 486 Score = 634 bits (1635), Expect = 0.0 Identities = 308/481 (64%), Positives = 382/481 (79%), Gaps = 2/481 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 + L+D LFRQQ +I G WVDAD G T++V NP+ +ILGTVP M AETR AI AA + Sbjct: 4 VNLQDQNLFRQQCYIGGQWVDADGGATLEVVNPSDQQILGTVPDMAEAETRGAIAAAREG 63 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 WR TA ER L RWYEL++ QDDLGRLMTLEQGKPL EAKGEIAYAA F++WFA Sbjct: 64 FEVWRKKTAAERGEILYRWYELMMALQDDLGRLMTLEQGKPLPEAKGEIAYAAGFLKWFA 123 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EE++R YGD IP +P + ++VIKQP+GV+ AITPWNFP+AMITRKAG ALAAGC+MV+K Sbjct: 124 EESRRAYGDTIPAAKPGQHIVVIKQPVGVSVAITPWNFPSAMITRKAGAALAAGCSMVVK 183 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240 PA++TPFSALAL EL RAG+P GVL+V+TG A IG LTS+ VRKLSFTGSTE+GR+ Sbjct: 184 PAAETPFSALALAELGERAGLPNGVLNVITGDAVRIGQTLTSSATVRKLSFTGSTEVGRK 243 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 LMA+CA+ I+K+SLELGGNAPF+VFDDADLDKAVEGA+ SK+RN GQTCVCANR +Q+ Sbjct: 244 LMAQCAEHIQKISLELGGNAPFLVFDDADLDKAVEGAMASKFRNTGQTCVCANRFLVQEG 303 Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKS 360 V+DAF EKLK A+ L++GNGLEEG LI++ AV KV EH+ DA+ KGA L+ GG++ Sbjct: 304 VHDAFVEKLKTAMETLRVGNGLEEGVNQSALINQAAVDKVDEHLRDAVGKGARLILGGEA 363 Query: 361 --MEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 + G + +P +L V D + EETFGP+A + +F+ E E I ++NDT +GLASYFY+ Sbjct: 364 HPLGGTYVQPALLTGVTPDMQLCHEETFGPVAAVMKFQTEEEAIRLANDTPYGLASYFYS 423 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 RD+ RV+RVAEALE G+VG+N GLISN VAPFGG+K SG+GREGSKYG+E+YLE+KYLC+ Sbjct: 424 RDIHRVWRVAEALEAGIVGINEGLISNPVAPFGGVKESGIGREGSKYGMEEYLEVKYLCM 483 Query: 479 G 479 G Sbjct: 484 G 484 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: 696 Number of extensions: 18 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: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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 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