Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_041099671.1 SUTH_RS12545 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >NCBI__GCF_000828635.1:WP_041099671.1 Length = 505 Score = 243 bits (620), Expect = 1e-68 Identities = 165/472 (34%), Positives = 226/472 (47%), Gaps = 8/472 (1%) Query: 12 HLINGRWEIGTTTGIST--NPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQR 69 H ING + G T + NP++ R V + A A R + AV AA A W + PQR Sbjct: 14 HWINGHADAGAGTRVGEVFNPAEGR-VARQVALATRADVDRAVAAARAAFADWGSAAPQR 72 Query: 70 RADVLDMIGSELLARKDELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELL 129 RA V+ + ++ LL+ E GKTLP+ + EV R ++ +F G ++G+ Sbjct: 73 RARVMFKFRDLVDQYSTDIAKLLSAEHGKTLPDALGEVQRGLEVIEFACGIPQLLKGQHS 132 Query: 130 ASVRQGVQVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWA 189 + G+ R P+GV I P+NFPF +P W ALA GNT + KP+E P+ Sbjct: 133 HGIGGGIDHWNQRMPLGVTAGITPFNFPFMVPMWMAPMALACGNTFILKPSERDPSPSLF 192 Query: 190 LAEIISRSGLPAGAFNLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAK 249 AE++ +GLPAGAFN+I G +E L++HP V+A+SF GS I + Sbjct: 193 AAELLREAGLPAGAFNVIQGD-KEAVDALLEHPFVSAVSFVGSTPIAKYIQAHGIAHGKR 251 Query: 250 VQLEMGGKNPLIVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRN 309 VQ G KN ++V+ DADLD A D + +Y S G+RC A S + D VAR+ Sbjct: 252 VQALGGAKNHMVVMPDADLDGAADALIGAAYGSAGERCMAISVAVAVGSCADDLVARVLA 311 Query: 310 RLASLKVGHALERGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGER--LERPTPGHY 367 R LKVG EMGP+V + GYI EGA+ V G G + Sbjct: 312 RAKKLKVGAGDAANVEMGPLVTAVHRDKVAGYIAAGVQEGAKLVLDGREGLTGELAQGFF 371 Query: 368 MSPALF-LARPEHRVAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAM 426 ++P LF P + +EEIFGPV CV+R + A+ L N F T A Sbjct: 372 INPTLFDNVTPNMSIYQEEIFGPVLCVVRVPTFAAAVELINRHTFANGVACFTRDGGTAQ 431 Query: 427 HFKRHAAVGMTMVNLPTAGVDFHVPFGGRKESSYGARE-QGRYAAEFYTTVK 477 F + VGM +N+P FGG K S +G G FYT K Sbjct: 432 AFIQKIEVGMVGINVPIPVPMAWHSFGGWKASLFGDHHIYGEEGVRFYTRYK 483 Lambda K H 0.320 0.135 0.400 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: 587 Number of extensions: 35 Number of successful extensions: 4 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: 483 Length of database: 505 Length adjustment: 34 Effective length of query: 449 Effective length of database: 471 Effective search space: 211479 Effective search space used: 211479 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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