Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_041098592.1 SUTH_RS08615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000828635.1:WP_041098592.1 Length = 480 Score = 669 bits (1727), Expect = 0.0 Identities = 329/481 (68%), Positives = 392/481 (81%), Gaps = 1/481 (0%) Query: 3 LKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP 62 +K+ +L R ++G W+ A G T+ + NPATGE +GSVP GAAETRRAI+AA A Sbjct: 1 MKNPELLRNACLINGEWLAA-TGATLDIRNPATGEAVGSVPGFGAAETRRAIDAAHAAFH 59 Query: 63 AWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEE 122 WRA TA ERA LRRWF+LM+ENQ+DLARLMT EQGKPLAEA+GEIAYAASF+EWF EE Sbjct: 60 PWRAKTAAERAKILRRWFELMMENQEDLARLMTQEQGKPLAEARGEIAYAASFIEWFAEE 119 Query: 123 AKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPA 182 A+RIYGD IP D+R+IV+KQP+GV AAITPWNFP+AMITRK PALAAGCTMV+KPA Sbjct: 120 ARRIYGDVIPSPLADRRLIVLKQPVGVCAAITPWNFPAAMITRKVAPALAAGCTMVVKPA 179 Query: 183 SQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLM 242 QTP SALALA L ++AG+P GV +VVTG +GGELTSNP V KL+FTGSTEIGR LM Sbjct: 180 EQTPLSALALAWLGQQAGLPPGVLNVVTGEPVAIGGELTSNPKVLKLSFTGSTEIGRLLM 239 Query: 243 AECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVY 302 +CA IKK+SLELGGNAPFIVFDDADLDAAV GA++SKYRN GQTCVC NR VQ+GV+ Sbjct: 240 GQCAPTIKKMSLELGGNAPFIVFDDADLDAAVAGAMLSKYRNTGQTCVCTNRFLVQEGVH 299 Query: 303 DAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHA 362 DAF +L AAVA L +G GLE GVT GPLID +AKVEE +ADA++KGA+V+ GGK HA Sbjct: 300 DAFAQRLAAAVAGLKVGYGLEEGVTQGPLIDGAGLAKVEELLADALAKGARVLCGGKRHA 359 Query: 363 LGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARD 422 GGTFFEPT+L ++++E FGP+AP+F FKDEA+ I M+NDTEFGLA+YF++RD Sbjct: 360 KGGTFFEPTVLAGATPAMRLAREEIFGPVAPIFSFKDEADAIRMANDTEFGLAAYFFSRD 419 Query: 423 LARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGG 482 +AR +RV E L+YGMVGIN+G+ISNEVAPFGG+K SGLGREGSKYGIE+YLEIKYL + G Sbjct: 420 IARAWRVGEALDYGMVGINSGMISNEVAPFGGVKQSGLGREGSKYGIEEYLEIKYLAMAG 479 Query: 483 I 483 + Sbjct: 480 L 480 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: 724 Number of extensions: 17 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: 480 Length adjustment: 34 Effective length of query: 449 Effective length of database: 446 Effective search space: 200254 Effective search space used: 200254 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