Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 218 bits (554), Expect = 5e-61 Identities = 151/487 (31%), Positives = 236/487 (48%), Gaps = 42/487 (8%) Query: 39 LIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERA 98 LI++G+ + + +PA + + DL + A+ +A AF W E+RA Sbjct: 6 LIVDGKPLAMAETFPVIDPATGRPFADAPLASTADL-DAAVAAARRAFPGWAATPIEDRA 64 Query: 99 NILVKAAAIIRRRKHEFSAWLVHEAGKP-------------WKEADADTAEAIDFLEYYA 145 ++ A I K E + L E GKP W A A A+D L+ Sbjct: 65 AAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKDDD 124 Query: 146 RQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLK 205 +E++R P+GV +ISPWNF + I + + +V GNTVV+K Sbjct: 125 SVRVEVHR----------------KPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMK 168 Query: 206 PASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVR 265 P+S TP+ A + VE+ +A LP GV+N V G E+G + HP I FTGS G Sbjct: 169 PSSFTPLAALRMVEIA-NAHLPPGVLNSVTGE-VEIGRAIASHPGIDKIVFTGSTPTG-- 224 Query: 266 LYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSR 325 +++ G +LKR+ +E+GG D +V DAD+D A I AFG SGQ C+A R Sbjct: 225 ----RSIMADGAANLKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKR 280 Query: 326 AVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKE-GRL 384 +H+ ++D + EK +A+ VG ++ + GPV + K F+ + + + + GR Sbjct: 281 VYVHESIHDALAEKLAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRF 340 Query: 385 MTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGL 444 + GGE G+F +++ D+ I+ EE FGP++ + +D + AL AN E GL Sbjct: 341 LAGGEAREGDGYFFPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGL 400 Query: 445 TGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLAL 504 G+V + + A + G ++ N + +I PFGG K SG ++ G L Sbjct: 401 GGSVWSADPAAALAFAQRLEAGTVWVNDH--ASISPDVPFGGAKQSGVGTEFGLYG-LEE 457 Query: 505 HMQAKTV 511 +MQ +TV Sbjct: 458 YMQLQTV 464 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: 589 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: 515 Length of database: 469 Length adjustment: 34 Effective length of query: 481 Effective length of database: 435 Effective search space: 209235 Effective search space used: 209235 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 17 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