Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_040513649.1 J416_RS13265 betaine-aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000359605.1:WP_040513649.1 Length = 484 Score = 245 bits (626), Expect = 2e-69 Identities = 143/466 (30%), Positives = 243/466 (52%), Gaps = 23/466 (4%) Query: 41 INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQT--WRNVNPEERA 98 +N + T D I +N +++ + + ++ A+ AI +A +AF W+N + ER Sbjct: 8 VNAQSGNTRDIINPYN----QEVIATAVEGDESDAKAAIAAARQAFDQGDWKNTSATERG 63 Query: 99 NILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEIL 158 I+ K A I R K E + + GK +E+ D + YYA I G EI+ Sbjct: 64 KIVRKIADFIERDKEELAYLESLDTGKTVEESRGDMDDIAGVFHYYAE--IADKDGGEII 121 Query: 159 SRP--GEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAK 216 P ++ + P+GV I+PWN+ L +VTGNT+++KP+ TP+ K Sbjct: 122 ESPLPNSISKVVHEPVGVCGQITPWNYPLLQASWKLAPALVTGNTLIMKPSEITPLTTVK 181 Query: 217 FVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPG 276 +++E+AG+P GV N V G+G+ G L + LI+FTG G ++ + A Sbjct: 182 VFKLIEEAGVPAGVANLVLGAGSTTGAELSESKDVDLISFTGGIATGKKIMKAAT----- 236 Query: 277 QNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEV 336 +++K+ +E+GGK+ ++ D D + A + + F +GQ CSAG+R ++ + ++D+ Sbjct: 237 -DNVKKTALELGGKNPNIIFADTDFETAVDQAMNGVFFHAGQICSAGTRLIVEESIHDQF 295 Query: 337 LEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGG-----EGD 391 +E V KN+ +G + D MGP+I ++ K++ Y+E GKKEG + G + + Sbjct: 296 VEALVNRVKNIKLGSGFDDDTQMGPLISKEHLNKVIDYVETGKKEGVTVEVGGKQPEDPE 355 Query: 392 SSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITR 451 GFF PT++ + ++QEE FGPV+ K + D A+++AN++ YGL GAV T Sbjct: 356 LQDGFFYLPTVLTGCTTDMDVVQEEGFGPVITVEKFSTEDEAVQLANDSIYGLAGAVFTN 415 Query: 452 NRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497 N A E+ + +G ++ N + P+GG+K SG + G Sbjct: 416 NIAKAERCAQAMRMGTVWINE--MNVYFPHAPWGGYKQSGIGRELG 459 Lambda K H 0.316 0.134 0.388 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: 638 Number of extensions: 35 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: 515 Length of database: 484 Length adjustment: 34 Effective length of query: 481 Effective length of database: 450 Effective search space: 216450 Effective search space used: 216450 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 (21.6 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