Align succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_012566781.1 RC1_RS07630 succinate-semialdehyde dehydrogenase I
Query= reanno::pseudo3_N2E3:AO353_11505 (480 letters) >NCBI__GCF_000016185.1:WP_012566781.1 Length = 508 Score = 709 bits (1829), Expect = 0.0 Identities = 345/479 (72%), Positives = 409/479 (85%), Gaps = 2/479 (0%) Query: 3 LKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKALP 62 L D LFRQ F+DG W+ AD+G+TI VTNPA G LG+VP MGAAE RRAI AA++A P Sbjct: 26 LSDPGLFRQDCFVDGQWIGADSGKTIAVTNPADGSTLGSVPAMGAAEARRAIAAAERAWP 85 Query: 63 AWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEE 122 AWR TAKERA LRRW+EL++ +Q+DLAR+MT EQGKPLAE++GEIVYAA+F+EWFAEE Sbjct: 86 AWRTKTAKERAQVLRRWYELMLAHQEDLARIMTAEQGKPLAESRGEIVYAANFLEWFAEE 145 Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 AKR+YGDVIP H+P R++V+K+P+GVTAAITPWNFPAAMITRKAGPALAAGC MV+KPA Sbjct: 146 AKRVYGDVIPTHRPGSRIVVVKEPVGVTAAITPWNFPAAMITRKAGPALAAGCPMVVKPA 205 Query: 183 SQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLM 242 S TP+SA A+A LA+RAG+P GVLSVVTGSAG IG E TSNP VRKLSFTGSTEIG+ LM Sbjct: 206 SYTPFSALAMAVLAERAGVPPGVLSVVTGSAGAIGGEFTSNPAVRKLSFTGSTEIGKTLM 265 Query: 243 AECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVY 302 A+CA +KK+SLELGGNAPFIVFDDADLD AV+GAI SKYRN GQTCVCANRL +QD VY Sbjct: 266 AQCAGTVKKLSLELGGNAPFIVFDDADLDAAVQGAIASKYRNTGQTCVCANRLLVQDGVY 325 Query: 303 DAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGK--V 360 DAFA +L AV LK+ NGLE+G T GPLID AV KV+EHI DA+SKGA ++ GG+ Sbjct: 326 DAFAARLADAVRGLKVANGLEDGATQGPLIDMAAVEKVEEHIRDAVSKGARIVTGGRRHA 385 Query: 361 MEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420 + G+FFEPT+L +V + AVA+EETFGP+APLFRFKDEAE I ++N TE+GLA+YFYARD Sbjct: 386 LGGSFFEPTVLADVTPAMAVAREETFGPVAPLFRFKDEAEAIHLANATEYGLAAYFYARD 445 Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479 LGRV+RVAEALEYG++G+N G+IS EVAPFGG+K SGLGREGSKYG+++YLEIKYL +G Sbjct: 446 LGRVWRVAEALEYGIIGINEGIISTEVAPFGGMKESGLGREGSKYGLDEYLEIKYLLMG 504 Lambda K H 0.317 0.135 0.389 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: 759 Number of extensions: 23 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: 508 Length adjustment: 34 Effective length of query: 446 Effective length of database: 474 Effective search space: 211404 Effective search space used: 211404 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