Align Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (uncharacterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases
Query= curated2:O32507 (477 letters) >FitnessBrowser__Cola:Echvi_0535 Length = 514 Score = 162 bits (409), Expect = 3e-44 Identities = 123/449 (27%), Positives = 219/449 (48%), Gaps = 15/449 (3%) Query: 16 ATVNPYTGETVKTFPFLESAEIPALIERADQAYREWGQRPVTERAAIMRRAAELMLERTD 75 ++ +P G+ + ++++A++A++ W + P +R ++R+ + + Sbjct: 38 SSYSPVDGKELGKVQMTTRESYEKVLDQAEKAFKAWRKVPAPQRGEVVRQIGIELRNKKS 97 Query: 76 ELASLITLEMGKLLREAKGEVALAASILNY-YGEQGPSFLEPKTIPVPQGEAAVLHAPLG 134 L L++ EMGK +E GEV I ++ G + P PLG Sbjct: 98 LLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLG 157 Query: 135 VLLGIEPWNYPLYQVVRFAAPNLVVGNTVLLKHSELCPQSALALE----QLFHDAGVPQG 190 ++ I +N+P+ V G+ + K SE P +++A + +F+ G P+G Sbjct: 158 IVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQLIAADVFNRNGFPEG 217 Query: 191 AYTNLFLRIADIEQVIAH-PAVQGVSLTGSERAGASVAELAGRHLKKCVLELGGSDPFIV 249 T+L + A++ + P V +S TGS + G SV E G L K +LELGG++ I+ Sbjct: 218 I-TSLLIGGANVGAFLTQDPRVALISATGSTQMGKSVGETVGGRLGKVLLELGGNNAIII 276 Query: 250 LDAEDLDTTVKAAATGRLSNTGQACIAAKRLMVVDDLYDEFVSRLGQTFSAFVPGDPADP 309 + DLD ++ A G + GQ C + +RL++ + +++E R+ +S G+P D Sbjct: 277 TEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERMVAAYSKLTIGNPLDE 336 Query: 310 STRLGPLSSEQAARD-LQAQVQDAIDKGATVVAGG--QRPEH-PGAFVQPTVLTDVTPDM 365 +GPL + A ++ L A + + G VVAGG + E+ G +V+P+V + Sbjct: 337 DNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYVSGCYVRPSVF-EAENHF 395 Query: 366 RAYHEELFGPVAVVYRVRDEDEAVALANASTYGLGGAVFSSDLDRAQRV--AERLDTGMV 423 + +E FGP+ + + + DEA+A+ N GL A+ ++++ A+R +E D G+ Sbjct: 396 QIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMREAERYLSSEGSDCGIS 455 Query: 424 WINHPTSSA-ADLPFGGVKRSGFGRELSS 451 +N TS A FGG K +G GRE S Sbjct: 456 NVNIGTSGAEIGGAFGGEKETGGGRESGS 484 Lambda K H 0.317 0.133 0.384 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: 566 Number of extensions: 35 Number of successful extensions: 4 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: 477 Length of database: 514 Length adjustment: 34 Effective length of query: 443 Effective length of database: 480 Effective search space: 212640 Effective search space used: 212640 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 17 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