Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_012708927.1 NGR_RS23205 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000018545.1:WP_012708927.1 Length = 477 Score = 278 bits (710), Expect = 4e-79 Identities = 170/475 (35%), Positives = 250/475 (52%), Gaps = 13/475 (2%) Query: 40 VINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99 +I GE V + I ++NP++ +VVG ++AS E A AI AA AF W + ER A Sbjct: 7 LIAGEWVGGDG-IANVNPSNTNDVVGEYARASAEDASAAIAAAKAAFPAWSRSGILERHA 65 Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159 +L + A ++ RK E LL +E GK E +T A +++A + + LA + Sbjct: 66 ILRKTADEILARKDELGRLLSREEGKTLAEGIGETIRASQIFDFFAGECLRLAGETLPSV 125 Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219 R + P GV +I PWNF AI A + GNTVV KPA P + V+ Sbjct: 126 RPNIGVEISREPVGVVGIITPWNFPIAIPAWKIAPALAYGNTVVFKPAELVPGCSWAIVD 185 Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279 +L +GLPKGV+N V G G+ VG ++D P ITFTGS G R+ +H Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTGTGKRV------ALASVEH 239 Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339 ++ EMGGK+ VV +DAD+ +A ++ SAF GQ+C+A SR +V E ++D+ + Sbjct: 240 NRKFQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRVIVTEGIHDKFVAA 299 Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDDSKGY 396 + E + V A ++GPV+DQ ++ YI IGKQEG +L GG D+ G+ Sbjct: 300 MGERMKGLVVDDALKAGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGELISRDTPGF 359 Query: 397 FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHI 456 +++P +F + R+ +EEIFGPV A +V D++EAL VAN+T +GL+ + T + KH Sbjct: 360 YLQPALFTEATNAMRISREEIFGPVAAVIRVKDYEEALNVANDTPFGLSAGIATTSLKHA 419 Query: 457 ERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510 K+ G + N G V +H PFGG K S + G + KT Sbjct: 420 THFKRNSEAGMVMVNLPTAG--VDFHVPFGGRKGSSHGPREQGKYAAEFYTTVKT 472 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: 590 Number of extensions: 42 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: 477 Length adjustment: 34 Effective length of query: 481 Effective length of database: 443 Effective search space: 213083 Effective search space used: 213083 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