Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_012402638.1 BPHY_RS16780 betaine-aldehyde dehydrogenase
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000020045.1:WP_012402638.1 Length = 489 Score = 256 bits (654), Expect = 1e-72 Identities = 165/475 (34%), Positives = 242/475 (50%), Gaps = 28/475 (5%) Query: 32 YLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRY 91 Y+G DY +G +T +PA E ++ V +AS+ E+A+Q+A + W Sbjct: 10 YIGGDYVDATSGVTFDT------FDPATGE-LLATVQQASEADIERAVQSAREGQRAWAA 62 Query: 92 TSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADA-DTAEAIDFMEYYARQMIE 150 + +R+ +L RA +R R E + L +++ GKP E A D D +EYYA + Sbjct: 63 MTAMQRSRILRRAVDLLRERNDELAELEMRDTGKPIAETRAVDIVTGADVIEYYAG-LAT 121 Query: 151 LAKGKPVNSREGEKNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPA 207 +G+ + R +VYT P GVT I WN+ I + + GN ++ KP+ Sbjct: 122 AIEGQQIPLRA---ESFVYTRREPLGVTAGIGAWNYPIQIACWKSAPALAAGNAMIFKPS 178 Query: 208 SATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIF 267 TP+ A+K E+ E+G+P GV N V G G VG L HP + I+FTG E G ++ Sbjct: 179 EVTPLSASKLAEIYLEAGVPAGVFNVVQGDG-RVGAMLSAHPGIAKISFTGGVETGKKVM 237 Query: 268 ERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAV 327 A G LK V E+GGK +VV EDAD++ AA T+ F AGQ C+ G+R Sbjct: 238 SMA-----GGSSLKEVTMELGGKSPLVVFEDADLDRAADIAVTANFFSAGQVCTNGTRVF 292 Query: 328 VHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVS 386 VH+ V RVIE + KP GP+ DK++ +IE GK+EG RLV+ Sbjct: 293 VHQSVQPAFEARVIERVKRIRVGKPSDPSTNFGPLASAAQLDKVLGFIESGKREGARLVA 352 Query: 387 GGT----GDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEY 442 GG GD ++G +++PT+F+D ++++EEIFGPV++ D D+ +E AN+T Y Sbjct: 353 GGARIVEGDYARGQYVQPTVFSDCRDDMKIVREEIFGPVMSILSFVDEDDVIERANDTIY 412 Query: 443 GLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497 GL V+T N RA G + N G P GG+K SG + G Sbjct: 413 GLAAGVVTENLARAHRAIHRLEAGICWI--NTWGESPAEMPVGGYKQSGVGRENG 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: 601 Number of extensions: 30 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: 489 Length adjustment: 34 Effective length of query: 481 Effective length of database: 455 Effective search space: 218855 Effective search space used: 218855 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