Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= curated2:Q12QD2 (498 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 203 bits (517), Expect = 1e-56 Identities = 157/471 (33%), Positives = 233/471 (49%), Gaps = 22/471 (4%) Query: 12 QTQF-IAGQWLAGKGPSFSSV-NPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSL 69 +TQF I GQW++ G V +P +G ++ +A D A+T+AR AF WS Sbjct: 4 RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63 Query: 70 TERLVIVEAFAEQLKEHAELFARTIALETGKAL-WESRTEVGAMTGKIAISIKANAERTG 128 ER ++ E LK A+ A+TI LE G + R +VG+ T + K A+ Sbjct: 64 AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFP- 122 Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188 E + +K + + GVVA P+N+P H + AL AG TV+ KPSE+ P A Sbjct: 123 -FEEKVGNSK--VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNA 179 Query: 189 ELTMQLWQQAGLPNGVLNLLQG-EIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247 L ++ AG+P GV NL+ G G+A+ +H+ +D + FTGS+ G + + A Sbjct: 180 FLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRV-SELASAT 238 Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307 K +ALE+GG + II + A+ + AV ++ + +++SGQ CT R+ +P T +A A Sbjct: 239 VKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEA--A 296 Query: 308 KLLTSTAK-IALGDPFAE---TQPFFGAMISDKAA--AGMVKAQADIQAAGGVSLIELTQ 361 KL A+ +GDP AE P M D+ G A+ GG L E Sbjct: 297 KLAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPE--G 354 Query: 362 VTPGLGFVTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLA 420 V P +V P I V S +A EE FGP+L + Y D + A+ AN T +GL+ G+ + Sbjct: 355 VNPDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWS 414 Query: 421 DSETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYAAD 471 ++ + RR+R G V N + APFGG SGN R Y + Sbjct: 415 ATDEHAEQVARRMRTGQVEINGGT--FNMYAPFGGYKQSGNGRELGKYGLE 463 Lambda K H 0.317 0.133 0.390 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: 561 Number of extensions: 33 Number of successful extensions: 6 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: 498 Length of database: 479 Length adjustment: 34 Effective length of query: 464 Effective length of database: 445 Effective search space: 206480 Effective search space used: 206480 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