Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_072908502.1 BUB13_RS10015 1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_900142125.1:WP_072908502.1 Length = 549 Score = 167 bits (422), Expect = 1e-45 Identities = 142/479 (29%), Positives = 228/479 (47%), Gaps = 33/479 (6%) Query: 24 PADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEFA 83 P D L + +V+ AI+ A+A W +R +I LKA +L+ + + Sbjct: 66 PHDHSIELGQYHKAGPKEVQMAIDAAMAAKPVWESLRWEERSAIFLKAADLL---SGPYR 122 Query: 84 LLMTLEEGKTLKDSMFEVT-----RSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEP 138 L+ + + F+ + L+F A +I + + + + P Sbjct: 123 FLINAATMLNISKNPFQAEIDSACELIDFLRFNVFFASEIYREQPMYSSKDIWNYVQHRP 182 Query: 139 L-GVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGV 197 L G V + P+NF +PA+ GNT V KPA+ +++L +AGLP+GV Sbjct: 183 LEGFVFAVAPFNFTAISGNLPTSPAIM-GNTVVWKPASSAVFAPYYFMKLLQEAGLPDGV 241 Query: 198 VNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVG------NKNRMTRIQLELG 251 +N V G GS+VGDTI++ + + FTGST V + ++K +G + RI E G Sbjct: 242 INFVPGSGSDVGDTILASPDFNGIHFTGSTPVFQSMWKEIGANLAKDHYKTYPRIVGETG 301 Query: 252 GKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWR 311 GK+ ++ SA++ A VRG F GQ C+A SR + + + K +L VK Sbjct: 302 GKDFIFAHSSANVAALATAMVRGAFEYQGQKCSAASRTYLPESL----KDAVLAEVKNQV 357 Query: 312 VGPGTEDV-DMG----PVVDEGQFKKDLEYIEYGKNV-GAKLIYGGNIIPGKGYFLEPTI 365 T DV D G V+D+G FK EYI+Y K A+++ GG KG+F+EPT+ Sbjct: 358 SRIKTGDVCDFGNFFNAVIDKGAFKSITEYIDYAKTADDAEIVIGGGYDDSKGWFIEPTL 417 Query: 366 FEGVTSDMRLFKEEIFGPVLSVTEAKD--LDEAIRLVNAVD-YGHTAGIVASDIKAINEF 422 + +EEIFGPVL+V D ++ + L + + T + A + AI+ Sbjct: 418 IVTTNPKFKTMEEEIFGPVLTVYCYPDAEYEQTLELCDQTSPFSLTGAVFAQERTAISLA 477 Query: 423 VSRVE--AGVIKVN-KPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 ++++E +G +N KPT + Q PFGG + SG T K + L + +T+ E + Sbjct: 478 LTKLENASGNFYINDKPTGAVVGQQPFGGGRASG-TNDKAGSKQNLMRWASVRTIKENF 535 Lambda K H 0.316 0.135 0.389 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: 668 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: 478 Length of database: 549 Length adjustment: 35 Effective length of query: 443 Effective length of database: 514 Effective search space: 227702 Effective search space used: 227702 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