Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_025274016.1 HALAL_RS0110770 betaine-aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000527155.1:WP_025274016.1 Length = 470 Score = 232 bits (591), Expect = 3e-65 Identities = 170/477 (35%), Positives = 239/477 (50%), Gaps = 29/477 (6%) Query: 37 HYPLYIGGEWVDTKERMV--SLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWP 94 HY L+I GE+V+ V S+NP+ +E+ T A AG + A+ AA KA W P Sbjct: 18 HYGLFIDGEFVEADGDQVEASINPATGAELF-TYAGAGSTDVVRAVAAARKAQADWAALP 76 Query: 95 QEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALRYR 153 +R + L + A L++ R RE + GK E+ D+ +A Y+A A + Sbjct: 77 GLERGKYLYRIARLLQERGREFAVAESMDNGKPIRESRDFDIPQAAQHFFYHAGWADKLD 136 Query: 154 YPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAV 213 Y PG PLG I PWNFP+ + I +A GNTV+ KPAE Sbjct: 137 YVR------PGAQ------PLGVAGQIIPWNFPLLMLAWKIAPALAAGNTVVLKPAETTP 184 Query: 214 VVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAG 273 + K E+ EA P GVVN + G G + G LVE + + FTGS VG +I ++ Sbjct: 185 LTALKFAELCQEAELPRGVVNIVGG-GPQTGTALVESDVEK-LAFTGSTGVGRRIAQSIA 242 Query: 274 RLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQG 333 KR +E GGK A +V + A D A EGV+ + QG C A SRL++ + Sbjct: 243 GSD------KRLTLELGGKGANVVFDDAALDQAVEGVLKGVFFNQGHVCCAGSRLLVQEN 296 Query: 334 AYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKR 391 E V+ER+ R L +G P ++N D+G V S Q ++ +E G+ EG +L G Sbjct: 297 IAEEVVERLKTRLSTLRLGDPLDKNTDIGAVNSGAQLDRIRQLVEQGREEGARLWDTGTE 356 Query: 392 LEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYS 451 L EG++ PT+FT+V +AQEEIFGPVLSV+ + EA+ AN+TPYGL GV++ Sbjct: 357 LPTEGFWHRPTIFTDVQQSHSVAQEEIFGPVLSVLTFRTPQEAMVKANNTPYGLAAGVWT 416 Query: 452 RKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLE 508 L WA + G ++ N PFGG K SG + G L L +L+ Sbjct: 417 SDAAKLNWAADKLRAGIVWAN--TYNRFDPASPFGGMKESG-YGREGGLQGLEAYLK 470 Lambda K H 0.319 0.137 0.403 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: 570 Number of extensions: 25 Number of successful extensions: 5 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: 516 Length of database: 470 Length adjustment: 34 Effective length of query: 482 Effective length of database: 436 Effective search space: 210152 Effective search space used: 210152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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