Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate PfGW456L13_2690 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= SwissProt::P94391 (515 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2690 Length = 502 Score = 260 bits (665), Expect = 7e-74 Identities = 167/481 (34%), Positives = 245/481 (50%), Gaps = 20/481 (4%) Query: 32 YLGKDYPLVINGERVE-TEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFE--E 88 +LGK + I G VE ++ + + E ++ R+ + + ++A+QAA F+ Sbjct: 21 FLGKVQKMFIGGAWVEASDGQTSDVVEPSTEGLITRIPMGTTDDLDRAVQAARAQFDGGA 80 Query: 89 WRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQ 147 WR P ER ++ R A + + E + + + GK A D D +D + Y+A Sbjct: 81 WRQAKPAERERMMQRLADLIEQNAAELAQIESIDMGKSVAFAKDVDIQGTVDTLRYFAGW 140 Query: 148 MIELAKGKPVNSREGEKNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVL 204 +L S G N YT GV I PWNF MA A + TG TVV+ Sbjct: 141 ATKLHGRTVEPSLPG--NYLAYTRKEAVGVVGAIVPWNFPLQTMAWKLGAALATGCTVVV 198 Query: 205 KPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGT 264 KPA T + A +F E+++E+G+P GV+N V G G+ VG + HP +TFTGS VG Sbjct: 199 KPAELTSLSALRFAELVQEAGIPDGVINIVTGRGSVVGAAMATHPGIDKLTFTGSTPVGQ 258 Query: 265 RIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGS 324 + A +KR+ E+GGK V+V DADI AAQ++ F +GQ C AG+ Sbjct: 259 TVGRAAL------DDMKRLTLELGGKSPVIVCADADIPAAAQAVANGVFFNSGQVCDAGT 312 Query: 325 RAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-R 383 RA +H VYD+ L +I T + A D ++GP++ ++ YIE GK EG Sbjct: 313 RAYIHSSVYDEFLRELITYTRTLKMAPGLDPDCFIGPLVSALQKQRVTEYIETGKAEGAE 372 Query: 384 LVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYG 443 LV GG D G+F++PTIFA+ R++QEEIFGPV+ D +EAL +AN++ YG Sbjct: 373 LVYGGQPVDGPGFFVEPTIFANCRNDMRIVQEEIFGPVLVTAPFDDEEEALALANDSPYG 432 Query: 444 LTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGP--DY 501 L A+ +N+ + G++Y N + G + PFGG+K SG G DY Sbjct: 433 LAAALYSNDLGKVHSLIPRLKAGSVYVNAH--GTLDPSMPFGGYKQSGFGKDLGAEQLDY 490 Query: 502 L 502 L Sbjct: 491 L 491 Lambda K H 0.316 0.133 0.379 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: 612 Number of extensions: 29 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: 515 Length of database: 502 Length adjustment: 34 Effective length of query: 481 Effective length of database: 468 Effective search space: 225108 Effective search space used: 225108 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