Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_012402879.1 BPHY_RS18040 aldehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >NCBI__GCF_000020045.1:WP_012402879.1 Length = 497 Score = 148 bits (374), Expect = 4e-40 Identities = 140/461 (30%), Positives = 216/461 (46%), Gaps = 37/461 (8%) Query: 104 DVQAAIESALEARKS--WASTPFADRASVFLKAADLISTKYRYDVMALTMHGQGK---NA 158 DV AA+ +A A + W+ R + LK A L+ ++ ++ L GK + Sbjct: 58 DVDAAVRAARRAFNAGVWSGLNPRQRKATLLKWASLMR-EHLDELALLETLDAGKPIGDT 116 Query: 159 WQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFVYAISPFNFTA 218 ++ AA ++F + A HH G+ R PL G V A+ P+NF Sbjct: 117 TSVDVPGAAYCVEWFAEAIDKVGGEVAPAD-HHLVGLVTR---EPL-GVVAAVVPWNFPI 171 Query: 219 IGGNLAGAPALM-GNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPGEAEEVTKTV 277 + + PAL GN VV KPS + + V Q+ EAG+P V VPG Sbjct: 172 LMASWKFGPALAAGNSVVLKPSEKSPLTAIRVAQLAREAGIPAGVFNVVPGGGGPGKLLA 231 Query: 278 LDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHLIHKSADIRN 337 L H D L FTGSTNV G++ + A + R+ E GGK+ +++ + Sbjct: 232 LHH-DVDCLAFTGSTNV-----GKLIMQYAGQS--NLKRVWLELGGKSPNIVLPDCPDLD 283 Query: 338 AAVQTVRGAFEYQ-GQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSDFTNFCGPV 396 A +T GA Y G+ C+A SR+ V I D FL+++ + A+S G P D G + Sbjct: 284 RAARTAAGAIFYNMGEMCTAGSRLLVHRDIKDVFLDKLVAAARSYAPGNPLDPKTSMGAI 343 Query: 397 IHEASFTKLAKVIDEAKNDPELELLAGGS--YDSSKGWYIQPTVYRTTNPDHPLLTRELF 454 + + ++ I+ + E +LL GG+ S G+YI+PTV+ + PD + E+F Sbjct: 344 VDQMQLDRVLGYIEAGR--AEAKLLHGGARVQQESGGFYIEPTVFEVSKPDAKIAREEIF 401 Query: 455 GPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRN-AAGNFY 513 GP+L V + EA +IA D YGL +V+ + L A++V R AG + Sbjct: 402 GPVLSVITFDTVDEA--VQIANDSD----YGLAAAVWTAN---LTTAHEVSRRLRAGTVW 452 Query: 514 INCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRS 554 +NC G + PFGG + SG N + S + L ++ L+S Sbjct: 453 VNCYDEGGDM-NFPFGGYKQSG-NGRDKSLHALEKYTELKS 491 Lambda K H 0.316 0.130 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: 629 Number of extensions: 31 Number of successful extensions: 3 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: 572 Length of database: 497 Length adjustment: 35 Effective length of query: 537 Effective length of database: 462 Effective search space: 248094 Effective search space used: 248094 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