Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_090446352.1 BLS63_RS15725 succinate-semialdehyde dehydrogenase I
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_900100495.1:WP_090446352.1 Length = 485 Score = 725 bits (1871), Expect = 0.0 Identities = 354/483 (73%), Positives = 413/483 (85%), Gaps = 3/483 (0%) Query: 1 MQLKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKA 60 +QL+D L RQQA+++G W +AD+G ++ NPA+GEI+G+VP +G ETRRAI AA A Sbjct: 3 LQLQDPSLLRQQAYVNGQWCEADSGARTEIRNPASGEIIGSVPNLGRGETRRAIAAAQAA 62 Query: 61 LPAWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA 120 PAWRALTAKERA +LR+W+ L++ NQ+DL R+MT EQGKPLAEA+GEIAYAASFIEWFA Sbjct: 63 QPAWRALTAKERANRLRQWFSLIMANQEDLARIMTAEQGKPLAEARGEIAYAASFIEWFA 122 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK 180 EEAKR YGDVIP H DKR++V K+ +GVTAAITPWNFP+AMITRKAGPALAAGC M++K Sbjct: 123 EEAKRAYGDVIPAHATDKRILVQKEAVGVTAAITPWNFPSAMITRKAGPALAAGCAMLLK 182 Query: 181 PASQTPFSALALVELAHRAGIPKGVLSVVTG---SAGDIGGELTSNPIVRKLSFTGSTEI 237 PA QTPFSALAL LA AGIP G+ SV+ ++ D+GGEL NPIVRKLSFTGST + Sbjct: 183 PAPQTPFSALALAALAECAGIPAGLFSVLPADVDASRDVGGELCENPIVRKLSFTGSTAV 242 Query: 238 GRQLMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYI 297 G +LM +CA +KK+SLELGGNAPFIVFDDADLD AVEGAIISKYRN GQTCVCANRLY+ Sbjct: 243 GIRLMQQCAPTLKKLSLELGGNAPFIVFDDADLDAAVEGAIISKYRNAGQTCVCANRLYV 302 Query: 298 QDSVYDAFAEKLKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAG 357 QD VY AFA KL AAVAKLK+GNG+EEG TTGPLI+ +AVAKV+ H+ DAL KGATL+AG Sbjct: 303 QDGVYQAFAAKLAAAVAKLKVGNGMEEGVTTGPLINAEAVAKVERHLRDALDKGATLVAG 362 Query: 358 GKSMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFY 417 G S+ GNFFEPTI+ V + AVA+EETFGPLAPLFRF DEAEVI +NDTEFGLA+YFY Sbjct: 363 GNSLGGNFFEPTIVSGVTAEMAVAREETFGPLAPLFRFSDEAEVIRQANDTEFGLAAYFY 422 Query: 418 ARDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477 ARDLGRVFRVAEALEYGMVG+NTGLIS EVAPFGG+K+SGLGREGSKYG+++YLEIKYLC Sbjct: 423 ARDLGRVFRVAEALEYGMVGINTGLISTEVAPFGGMKSSGLGREGSKYGLDEYLEIKYLC 482 Query: 478 LGI 480 LG+ Sbjct: 483 LGV 485 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: 747 Number of extensions: 15 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: 485 Length adjustment: 34 Effective length of query: 446 Effective length of database: 451 Effective search space: 201146 Effective search space used: 201146 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