Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Caulo:CCNA_00865 Length = 478 Score = 308 bits (790), Expect = 2e-88 Identities = 168/457 (36%), Positives = 256/457 (56%), Gaps = 7/457 (1%) Query: 22 INPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQE 81 +NP++ + V+AK+ + + +V A++ A F W+ R +L K G + + + Sbjct: 23 LNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKVGSTIIARSAD 82 Query: 82 FALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGV 141 L+ EEGKTL + + E R+ + K++ A + G+ L S P I T ++ +GV Sbjct: 83 IGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAVGV 142 Query: 142 VALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLV 201 LITPWNFP++IP WK APALA GNT VIKPA TP L +++++ G P GV N++ Sbjct: 143 YGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADIMAECGAPAGVFNML 202 Query: 202 VGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKS 261 G+GS +GD ++ ++ VSFTGS VG ++ R R+QLE+GGKN L V Sbjct: 203 FGRGS-MGDALIKHKDVDGVSFTGSQGVGAQV--AAAAVARQARVQLEMGGKNPLIVLDD 259 Query: 262 ADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTE-DVD 320 ADL A +A+ G F TGQ CTA+SRLI+ ++ +F L E+V RVG + + Sbjct: 260 ADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQ 319 Query: 321 MGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEPTIFEGVTSDMRLFKE 378 +GP V E Q + YI+ + G +++ GG+ I G+++ PT+ + MR+ E Sbjct: 320 IGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYVRPTLIADTQAGMRINNE 379 Query: 379 EIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTV 438 E+FGPV S K +EA+ + N V++G +AGI + +K F AG+ VN T Sbjct: 380 EVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHFQRYARAGMTMVNLATA 439 Query: 439 GLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 G++ PFGG K+S +E G A+EF+ + KT Y Sbjct: 440 GVDYHVPFGGTKSSSYGA-REQGFAAVEFFTQTKTSY 475 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: 578 Number of extensions: 31 Number of successful extensions: 6 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: 478 Length adjustment: 34 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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