Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_012709840.1 NGR_RS27930 NADP-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_000018545.1:WP_012709840.1 Length = 484 Score = 704 bits (1817), Expect = 0.0 Identities = 340/481 (70%), Positives = 407/481 (84%), Gaps = 2/481 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 M LKD LFRQ A + W++AD I+VNNPATGEI+G VPK+GAAET+ AIE A + Sbjct: 1 MNLKDPSLFRQAALVGENWIEADPQNAIEVNNPATGEIIGRVPKLGAAETKVAIETAARV 60 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 W TAKERA LRRWYEL+IEN+DDLG+++T+EQGKPLAEA GEI Y ASFIEWFA Sbjct: 61 QKEWAGRTAKERAAILRRWYELMIENKDDLGQILTIEQGKPLAEATGEIVYGASFIEWFA 120 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EE +R+YGD++PGHQ DKR++V+KQPIGV AAITPWNFP AMITRKAGPA AAGC MV+K Sbjct: 121 EEGRRVYGDLVPGHQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPAFAAGCAMVLK 180 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQ 240 PA+QTP+SA+A+ LA RAG+PKG+ SV+TGSA +IG E+TSNP VRKL+FTGSTE+G + Sbjct: 181 PAAQTPYSAIAIAVLAERAGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAE 240 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 L + A IKK+ LELGGNAPFIVFDDADLD AVEGA+I+K+RNNGQTCVCANRLY+Q+ Sbjct: 241 LYRQSAATIKKLGLELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRLYVQEG 300 Query: 301 VYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK- 359 VYDAF+EKL AAVAKLK GNG+E+GT GPLID+ A+ KV+EH+ADAL KGA ++ GG+ Sbjct: 301 VYDAFSEKLAAAVAKLKTGNGMEDGTILGPLIDKPALEKVEEHVADALAKGARVIQGGRR 360 Query: 360 -SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 ++ G+FFE T+L +V + AVA+EETFGP+APLFRFKDEA+VI +NDTEFGLASYFYA Sbjct: 361 HALGGSFFEATVLADVTQAMAVAREETFGPVAPLFRFKDEADVIRQANDTEFGLASYFYA 420 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 +DL RVFRVAEALEYGMVGVNTGLIS APFGG+K SGLGREGSKYGIE+++EIKY+CL Sbjct: 421 KDLARVFRVAEALEYGMVGVNTGLISTAEAPFGGVKFSGLGREGSKYGIEEFMEIKYVCL 480 Query: 479 G 479 G Sbjct: 481 G 481 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: 736 Number of extensions: 21 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: 484 Length adjustment: 34 Effective length of query: 446 Effective length of database: 450 Effective search space: 200700 Effective search space used: 200700 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 Apr 09 2024. 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