Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011612882.1 TERY_RS16535 L-glutamate gamma-semialdehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000014265.1:WP_011612882.1 Length = 993 Score = 273 bits (699), Expect = 2e-77 Identities = 162/462 (35%), Positives = 250/462 (54%), Gaps = 12/462 (2%) Query: 22 INPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQE 81 +NP++ V+ KI L + + ++AI A A F W +TP +R IL KA +LME+ E Sbjct: 522 LNPSNSKEVVGKIGLISVEQAEQAIQAAKAAFPSWKKTPVRERTRILRKAADLMEKRRHE 581 Query: 82 FALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKIS-GKTLPSADPNTRIFTVKEPLG 140 A M LE GK L EV+ + + ++Y ++ G A R + +P G Sbjct: 582 LAAWMVLEVGKPLNQGNAEVSEAIDFCRYYADEMERLEQGYNYDVAGETDRYYY--QPRG 639 Query: 141 VVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNL 200 + +I+PWNFPL+IP +L GN ++KPA + ++ +K+ E+L +AG P+GV Sbjct: 640 ISLVISPWNFPLAIPTGMTVSSLVTGNCTLLKPAAVSSVIASKISEILLEAGFPKGVFQF 699 Query: 201 VVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYK----LVGNKNRMTRIQLELGGKNAL 256 V G GS VGD +V ++ +++FTGS EVG IY L + + R+ E+GGKNA+ Sbjct: 700 VPGNGSTVGDFMVKHPSVNSITFTGSMEVGCHIYAQAAVLQPRQKHLKRVIAEMGGKNAI 759 Query: 257 YVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGT 316 VD+SADL A V FG +GQ C+A SR+++ +Y F RL+E + +G Sbjct: 760 IVDESADLDQAVAGVVYSAFGYSGQKCSACSRVVVLATIYDSFVNRLVEATRSLNIGDAE 819 Query: 317 E-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRL 375 + +GPV+DE K+ EYI GK I P GYF+ P IF+ V+ + Sbjct: 820 KPSTQVGPVIDEKAQKRIQEYIVKGKQEAEVAIEMS--APKDGYFVGPVIFKDVSPSATI 877 Query: 376 FKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNK 435 +EEIFGPVL+V +A + +A+ + N ++ T G+ + I + + E G + +N+ Sbjct: 878 AQEEIFGPVLAVMKADNFTQALEIANGTNFALTGGLYSRTPSHIEQAKAEFEVGNLYINR 937 Query: 436 PTVG-LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYE 476 G + + PFGGFK SG + K G D L +L+ +T+ E Sbjct: 938 GITGAIVSRQPFGGFKLSGVGS-KAGGPDYLLQFLEPRTITE 978 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: 1046 Number of extensions: 50 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 993 Length adjustment: 39 Effective length of query: 439 Effective length of database: 954 Effective search space: 418806 Effective search space used: 418806 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: 54 (25.4 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