Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 689 bits (1779), Expect = 0.0 Identities = 329/483 (68%), Positives = 405/483 (83%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 ++LKD L Q ++ W++AD+ + + V NPATGE++G+VP GA ETRRAI+AA+ + Sbjct: 2 IKLKDPGLLCQACFIQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGS 61 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 LPAWR+ TA +R+ LRRW DL++ENQ+DLA LMT EQGKPLAE++GEIAYAASF EWF Sbjct: 62 LPAWRSKTAAQRSAILRRWHDLLMENQEDLALLMTAEQGKPLAESRGEIAYAASFFEWFA 121 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EEAKRIYGD IP +R++VIKQP+GV AAITPWNFPSAMITRKAG ALAAGCTMV+K Sbjct: 122 EEAKRIYGDIIPQTIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVK 181 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240 PA+ TP+SALA+A+LA+ AG+P GVF+VVTGS+ +GGELT+NPIVRKLTFTGSTE+G++ Sbjct: 182 PATATPFSALAIAKLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKK 241 Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300 LM +CA +K+VS+ELGGNAPFIVFDDADLDAAVEGAL KYRN+GQTCVCANRLYVQ G Sbjct: 242 LMQDCAGTMKRVSMELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAG 301 Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360 VYD F +KL AVA L +GNG+E GV GPLID KAV VE HI DA+ KGAKV++GGK Sbjct: 302 VYDQFCEKLARAVATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKGAKVLAGGKR 361 Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420 HALGGTFF PT+L DV + LV+K+E FGP AP+F+F+ EAEV+ +NDTE+GLA+YF+ Sbjct: 362 HALGGTFFSPTVLADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFT 421 Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 RD+AR +RV E+LEYG++GIN+G+ISN VAPFGG+K SG GREGSKYG++DYLEIKY+C+ Sbjct: 422 RDMARTWRVGEKLEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 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: 695 Number of extensions: 9 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: 485 Length adjustment: 34 Effective length of query: 449 Effective length of database: 451 Effective search space: 202499 Effective search space used: 202499 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