Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067474647.1 BJL86_RS10335 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_001659785.1:WP_067474647.1 Length = 494 Score = 232 bits (592), Expect = 2e-65 Identities = 159/457 (34%), Positives = 234/457 (51%), Gaps = 31/457 (6%) Query: 55 INPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WRYTSPEERAAVLFRAAAKVRRRK 112 I PAD +V G VS+AS E AI AA +AF+ W ER L A ++RRRK Sbjct: 26 ICPADGTDV-GVVSEASTADTESAIAAARRAFDSRVWADRPAGERGDFLLDVAEQLRRRK 84 Query: 113 HEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEK-NQYVYTP 171 EF+ + GK EA+ D + I ++ + + + G+ V++ + ++ VY P Sbjct: 85 DEFARAEALDTGKRLVEAEGDMDDIIACFRFFGK-IADHDPGRLVDAGDNSVISRVVYEP 143 Query: 172 TGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGV 230 GV +I PWNF + A +AP + GN+ V+KPA TP ++V+++ GLP GV Sbjct: 144 IGVCGMITPWNFPL-LQASWKIAPALAAGNSFVIKPAELTPHTTILILDVIDKLGLPAGV 202 Query: 231 VNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGK 290 N V G G VG L HP L++FTG G +I E AA PG +K+V E+GGK Sbjct: 203 ANLVLGDGGTVGAPLSSHPDIDLVSFTGGLVTGRKIAEAAA---PG---IKKVALELGGK 256 Query: 291 DTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTA 350 + VV DAD + A + + F +G CSAG+R +V + + ++ ++ ++ E V Sbjct: 257 NPNVVFADADFDAAVDNALNAGFVDSGLVCSAGTRLIVQDTIAEKFVDALVRRAEGIVMG 316 Query: 351 KPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSG---GTGDDSKGYFIKPTIFADL 406 P + GP+I + DK+ Y++ G G RL +G G + KGYF PTI Sbjct: 317 GPLDENAETGPLISEAHRDKVTDYVKRGVDAGARLRTGGHWGGPEHEKGYFYAPTILDQC 376 Query: 407 DPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVG 466 + EE FGPV+ S +EA+E+AN+TEYGL GAV +++ R + G Sbjct: 377 TKDNPAVIEEGFGPVITVETFSTEEEAVEIANHTEYGLAGAVWSSDAGTANRVSRRLRHG 436 Query: 467 NLYFNRNCTGAIVGYHPF------GGFKMSGTDSKAG 497 ++ N YHP+ GGFKMSG + G Sbjct: 437 TIWIN--------DYHPYVPQAEWGGFKMSGVGRELG 465 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: 647 Number of extensions: 41 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: 494 Length adjustment: 34 Effective length of query: 481 Effective length of database: 460 Effective search space: 221260 Effective search space used: 221260 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