Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 290 bits (743), Expect = 6e-83 Identities = 179/469 (38%), Positives = 260/469 (55%), Gaps = 12/469 (2%) Query: 8 IAGEWVGGDGVANINPSN--TDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65 I G+WV DG A I+ N T+ V+ +A DA A AA AAFPAW+ ER A Sbjct: 9 IGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERGA 68 Query: 66 ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQ-IFEFFAGETLRLAGEVVPS 124 L+K AD + AR+DELGRL++ E G + + V+AG IF F A R+A E Sbjct: 69 FLQKIADGLKARQDELGRLIASEVGMPVK--LATRVQAGNPIFTFAA--CARIAAEGFAE 124 Query: 125 VRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIV 184 R G + + + P G V ITPWNFP+ A K+ AL G T+V KP+E+ P ++ + Sbjct: 125 ERIGQSL-VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183 Query: 185 DILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQ 244 +++ AGLP GV NLV G G VVG+A+ P + A++FTGSTA GKRVA + ++ Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243 Query: 245 LEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERI 304 LE+GGK+ VVL DADL+ AV+ V F ++GQ C+A +R++V + + A + Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303 Query: 305 KGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP-GFYLQP 363 + D L G+ +GP+V Q + I +GA+L GG P G+Y++P Sbjct: 304 AAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVRP 363 Query: 364 ALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFK 423 +F + ++REE+FGPV A++ +D EA A+AN T +GL++ + + A F Sbjct: 364 TVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFA 423 Query: 424 RNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKT 472 R AG V +N A + PFGG K S YG RE G++ E + ++ Sbjct: 424 RRLRAGQVDIN--GAFFNLLAPFGGFKQSGYG-RELGRHGVEDFLETQS 469 Lambda K H 0.317 0.134 0.391 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: 535 Number of extensions: 21 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: 477 Length of database: 476 Length adjustment: 33 Effective length of query: 444 Effective length of database: 443 Effective search space: 196692 Effective search space used: 196692 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 (21.7 bits) S2: 51 (24.3 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