Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_013840601.1 DESRU_RS02740 L-glutamate gamma-semialdehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000215085.1:WP_013840601.1 Length = 515 Score = 294 bits (753), Expect = 4e-84 Identities = 169/472 (35%), Positives = 248/472 (52%), Gaps = 16/472 (3%) Query: 15 SGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGEL 74 +GEE + +NP+ D V+ + + + K A+ A F WSR +R L KA + Sbjct: 48 TGEEVISLNPSASDQVVGYVAKASLQEAKLALESAQEAFARWSRVKPEERARYLFKAAAI 107 Query: 75 MEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFT 134 M + E + M E GK ++ + + + L+FYG +++ P RIF Sbjct: 108 MRRRKMELSAWMVFEAGKNWAEADGDTAEAIDFLEFYGREMCRLA-----EPQPLVRIFG 162 Query: 135 VKE-----PLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLS 189 PLGV +I PWNFPL+I A A+ GNT V+KPA+ TP++ AK +E+L Sbjct: 163 EDNRLKYIPLGVGLVIPPWNFPLAIMAGMTAAAIVTGNTVVLKPASNTPVIAAKFIEILQ 222 Query: 190 KAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIY----KLVGNKNRMTR 245 +AGLP+GVVN + G G +GD +VS I ++FTGS EVG RI K+V + + R Sbjct: 223 EAGLPDGVVNYLPGSGGAIGDYLVSSPQIRFINFTGSKEVGLRISELAAKMVPGQKAIKR 282 Query: 246 IQLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLE 305 + E+GGK+A+ VD S+DL AA V FG GQ C+A SR II DVY + + +++ Sbjct: 283 VVAEMGGKDAIIVDSSSDLEEAAAAIVASAFGFQGQKCSACSRAIILDDVYDRIVELVID 342 Query: 306 RVKKWRVGPGTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTI 365 + KK VGP ++ +GPV D K+ YIE GK G + G + GYF++PT+ Sbjct: 343 KTKKLTVGPAVDNYPVGPVTDSNSLKRIKSYIEIGKKEGTLQVGGETLEHMGGYFVQPTV 402 Query: 366 FEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSR 425 V + + +EEIFGPVL+V AKD A+ + N +YG T + + + + Sbjct: 403 ITDVPPNATIAQEEIFGPVLAVIRAKDFSHALDIANGTEYGLTGSVFSRNRANLERAARE 462 Query: 426 VEAGVIKVNKPTVGLELQA-PFGGFKNSGATTWKEMGEDALEFYLKEKTVYE 476 G + N+ G + PFGGF SG T K G D L + + K + E Sbjct: 463 FHVGNLYFNRKCTGALVGVHPFGGFNMSG-TDSKAGGRDYLLLFSQAKAISE 513 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: 611 Number of extensions: 32 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: 478 Length of database: 515 Length adjustment: 34 Effective length of query: 444 Effective length of database: 481 Effective search space: 213564 Effective search space used: 213564 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