Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 673 bits (1737), Expect = 0.0 Identities = 319/483 (66%), Positives = 402/483 (83%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 +++K+ LF + ++ WV AD+G+T+ V NPATG+I+G+VP GA ET+RAI AA+++ Sbjct: 2 LKIKNTALFCRHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANES 61 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 L AWR+ TA ER+ LR+W+DL++ENQ+DLA +MT EQGKPLAE++GEIAYAA+F EWF Sbjct: 62 LDAWRSKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFA 121 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EEAKR+YGD IP +R++VIKQP+GV AAITPWNFPSAMITRKAG ALAAGCTMVLK Sbjct: 122 EEAKRVYGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLK 181 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240 PA+ TP+SALA+A+L ++AG+PKGVF+VVTGS+ +GGELT+NPIVRKLTFTGST++G++ Sbjct: 182 PATATPFSALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKK 241 Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300 LM +CA +K++S+ELGGNAPFIVFDDAD+DAAVEGA+ KYRN+GQTCVCANR+YVQ G Sbjct: 242 LMRDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAG 301 Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360 VYD F KL AAV +L +GNG + GV GPLID AV VE HI DAV KG KV++GG Sbjct: 302 VYDEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTR 361 Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420 HALG TFF PTI+ DV + V+++ETFGPLAPVF+F E EV+ +NDTEFGLA+YFY Sbjct: 362 HALGRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYT 421 Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 RD+AR +R+ E+LEYG+VGIN+G+ISN VAPFGG+K SG GREGSKYG++DYLEIKY+C+ Sbjct: 422 RDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481 Query: 481 GGI 483 GI Sbjct: 482 AGI 484 Lambda K H 0.317 0.135 0.391 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: 702 Number of extensions: 12 Number of successful extensions: 1 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: 483 Length of database: 484 Length adjustment: 34 Effective length of query: 449 Effective length of database: 450 Effective search space: 202050 Effective search space used: 202050 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