Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= reanno::WCS417:GFF5420 (497 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 318 bits (816), Expect = 2e-91 Identities = 193/475 (40%), Positives = 266/475 (56%), Gaps = 17/475 (3%) Query: 23 YINGEYTAAVSGDTFECISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAK 82 YI+G++ + T E SP DG LLATV +AADA +AV AR F++ WS A+ Sbjct: 8 YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDA--WSVTPAAE 65 Query: 83 RKSAMLRFAALLKANAEELALLETLDMGKPISDSLNIDVPGAANALS-WSGEAIDKIYDE 141 R + + + LKA A+E+A TL+MG P S I V + +S D ++E Sbjct: 66 RAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPFEE 125 Query: 142 VAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAI 201 V RE VGVV AI PWN+PL K+ AL+ G +V+LKPSE +PL A Sbjct: 126 KVGNSK-----VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNAF 180 Query: 202 RIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNM 261 +A + AG+P GVFN++ GYG VG A+ H +VD + FTGST+ A + + + Sbjct: 181 LLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTR-AGTRVSELASATV 239 Query: 262 KRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPL 321 KRV LE GGKS I+ DA D A + G N G+ CTA +R+LV + + L Sbjct: 240 KRVALELGGKSAAIILDDA-DFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKL 298 Query: 322 VIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLE--ETG 379 +EA + ++ G+P+ +G L Q + V YI G A+G +L+ GG E Sbjct: 299 AVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNPD 358 Query: 380 GTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADIS 439 G YV+PTIF V IA+EEIFGPVLS+I++ E+AV+IAN T+YGLA VW+A Sbjct: 359 GYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDE 418 Query: 440 KAHLTAKALRAGSVWVNQYDGG--DMTAPFGGFKQSGNGRDKSLHAFDKYTELKA 492 A A+ +R G V +N GG +M APFGG+KQSGNGR+ + + + E KA Sbjct: 419 HAEQVARRMRTGQVEIN---GGTFNMYAPFGGYKQSGNGRELGKYGLEDFLEFKA 470 Lambda K H 0.316 0.132 0.386 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: 560 Number of extensions: 29 Number of successful extensions: 7 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: 497 Length of database: 479 Length adjustment: 34 Effective length of query: 463 Effective length of database: 445 Effective search space: 206035 Effective search space used: 206035 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 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