Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 265 bits (678), Expect = 2e-75 Identities = 164/488 (33%), Positives = 253/488 (51%), Gaps = 24/488 (4%) Query: 35 KDYPLVINGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WR 90 + Y ++I+G V++ + ++P D GRV A+ E ++A++AA +AF+E W Sbjct: 19 RSYSMLIDGAWVQSSSGETFACVDPYDNASW-GRVPAATVEDVDRAVRAARRAFDEGGWP 77 Query: 91 YTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIE 150 T P +RAA+L R A + E + + E GK E + Y A + E Sbjct: 78 QTLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYVAG-LAE 136 Query: 151 LAKGKPVNSREGEKNQYVYT-PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASA 209 +G+ + S + + P GV +I PWN +++ A + GNTVV+KP+ A Sbjct: 137 TIQGRTIESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEA 196 Query: 210 TPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFER 269 TP + E+ E+G P GV+N V G G G LVDH I FTGS G I ++ Sbjct: 197 TPTSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQ 256 Query: 270 AAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVH 329 AA + RV E+GGK ++ DADI+ A FG GQ C GSR +V Sbjct: 257 AA------ERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQ 310 Query: 330 EKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG 388 + +YD ++R+ T++ P V MGPV ++ + K++ Y+++G+ EG +V+GG Sbjct: 311 DSIYDDFVDRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGG 370 Query: 389 -----TGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYG 443 T + SKG F +PT+FA++ ++RL QEEIFGPV + + D DEA+++AN +++G Sbjct: 371 ARCMTTSELSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFG 430 Query: 444 LTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYL 502 L V TN+ R + G ++ N T + Y PFGGFK SG + GPD L Sbjct: 431 LAAGVWTNDVSRAHRMIRRVRSGTVWVN---TYRLTNYSVPFGGFKQSGIGREL-GPDAL 486 Query: 503 ALHMQAKT 510 + + K+ Sbjct: 487 DAYTEVKS 494 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: 565 Number of extensions: 27 Number of successful extensions: 4 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: 508 Length adjustment: 35 Effective length of query: 480 Effective length of database: 473 Effective search space: 227040 Effective search space used: 227040 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