Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011779095.1 MVAN_RS09340 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000015305.1:WP_011779095.1 Length = 488 Score = 266 bits (679), Expect = 2e-75 Identities = 173/457 (37%), Positives = 242/457 (52%), Gaps = 19/457 (4%) Query: 50 DKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIR 109 D + S NPAR +V S A + A+ +A A +W +R L+ AA I+ Sbjct: 21 DALVSVNPARPTVVVAEGSCAVASDVDAAVGAAAAAAPSWAATGMHQRGARLLAAAEIVE 80 Query: 110 RRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILS--RPGEQNRY 167 R + L E GK E + A L YY + + EI S RPGEQ Sbjct: 81 RNAERWGLELATEEGKTRAEGVGEVRRAAQILRYYGNEGDR--QAGEIYSSPRPGEQILV 138 Query: 168 FYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLP 227 P+GV ++P+NF +AI +V GNTVV KPAST P++A +F E L DAGLP Sbjct: 139 TRKPLGVVGVVTPFNFPIAIPAWKIAPALVYGNTVVWKPASTVPLLALRFAEALTDAGLP 198 Query: 228 KGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVR-PGQNHLKRVIVE 286 GV+N V G GA++GD +V+HP ITFTGS VG R+ AA P Q E Sbjct: 199 PGVLNLVVG-GADIGDAIVNHPGIDGITFTGSTGVGRRIAAAAAARGVPAQ-------AE 250 Query: 287 MGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKN 346 MGGK+ VV DADLDLA E +++ AF +GQKC+A SR ++ + D E +A A+ Sbjct: 251 MGGKNAAVVLDDADLDLAVEQVMLGAFRSTGQKCTATSRLIVTAGIADAFSEALLAQARA 310 Query: 347 LTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGG----EGDSSTGFFIQPT 401 L VGDP + MGPV+ + A + I + I+ +G ++TGG +G + G+F+ PT Sbjct: 311 LRVGDPVDDATQMGPVVSDSAQQSITAGIDTAVTQGATVLTGGRPYQDGALAEGYFVAPT 370 Query: 402 IIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKR 461 ++ + +E+FGPV+A +A D + A +AN++E+GL+ AV T++ QA Sbjct: 371 VVELGAAPVDVWTDELFGPVLAIRRATDAEEAFALANDSEFGLSAAVFTQDMTRALQAVE 430 Query: 462 EFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGG 498 VG L+ N GA + PFGG K SG K G Sbjct: 431 RIDVGVLHVNSESAGA-DPHVPFGGAKKSGLGPKEQG 466 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: 641 Number of extensions: 32 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: 488 Length adjustment: 34 Effective length of query: 481 Effective length of database: 454 Effective search space: 218374 Effective search space used: 218374 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