Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 370 bits (950), Expect = e-107 Identities = 199/475 (41%), Positives = 274/475 (57%), Gaps = 3/475 (0%) Query: 1 MANVTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE 60 M + +T LIDG+WV + + DV+NPA G I VA G A+ A+ AA Sbjct: 4 MTALNLVETAALIDGQWVRGEA--SFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALP 61 Query: 61 AWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADE 120 AW A ER A +R+ + L+ AD +A+LMT EQGKPL EA+ EV+ A I+WFA+E Sbjct: 62 AWAARTAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEE 121 Query: 121 GRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAP 180 +R YG +P G + +K+PVG AA PWNFP+ + RK+ ALA GC+ +VK Sbjct: 122 AKRAYGHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPA 181 Query: 181 EETPASPAALLRAFVDAGVPAGVIGLVYGD-PAEISSYLIPHPVIRKVTFTGSTPVGKQL 239 ETP S A+ R +AGVPAGV+ +V +E+ L +RK++FTGSTP+GK L Sbjct: 182 AETPLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVL 241 Query: 240 ASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSI 299 MK+ ++ELGG+AP IV +DAD+ AV A +K+RNAGQ C+ R +V + I Sbjct: 242 YQQCAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGI 301 Query: 300 RDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERI 359 D F L + LKVG G EG +G L N + LT + ++ A + GA + TGG+ Sbjct: 302 HDAFAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVH 361 Query: 360 GSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTR 419 G G+F+ PTV+ + +F E FGPVA I F+ EA+ AN PFGLA Y ++R Sbjct: 362 GLGGHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSR 421 Query: 420 SFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 + +++E GM+ IN+ PFGGVK+SG G EG E L+ YL TK Sbjct: 422 DVGRCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETK 476 Lambda K H 0.318 0.134 0.393 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: 664 Number of extensions: 36 Number of successful extensions: 3 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: 481 Length of database: 485 Length adjustment: 34 Effective length of query: 447 Effective length of database: 451 Effective search space: 201597 Effective search space used: 201597 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