Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 270 bits (689), Expect = 1e-76 Identities = 150/454 (33%), Positives = 248/454 (54%), Gaps = 1/454 (0%) Query: 28 IKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERANKLRRWFDLMIENQ 87 +K NP TGE++ + AI+ +A +WR L +RA+ +++ ++ +N Sbjct: 1 MKSINPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNT 60 Query: 88 DDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPGHQPDKRIIVIKQPI 147 D +++++E GK + E+K E+ A E++ E A+ + D K V+ P+ Sbjct: 61 DKYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPL 120 Query: 148 GVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALAELAERAGIPKGVFS 207 G+ A+ PWNFP + R A P L AG +LK AS P ALA+ E+ +AG P+GVF Sbjct: 121 GIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQ 180 Query: 208 VVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKVSLELGGNAPFIVFDD 267 + + +V + ++P V+ T TGS + G+++ A+ + IKK LELGG+ PFIV D Sbjct: 181 SLLIGSDKVAN-IIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKD 239 Query: 268 ADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAAVAKLNIGNGLEAGVT 327 AD+ A + A + N GQ+C+ A R ++ VYD F+ K+A+ G+ L+ Sbjct: 240 ADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAG 299 Query: 328 TGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTILVDVPKNALVSKDET 387 + ++ E + ++ KGA+V+ G G F +P IL + + ++E Sbjct: 300 YACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREEL 359 Query: 388 FGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQLEYGMVGINTGLISN 447 FGP+A VF+ D E IA++ND+ FGL + + +D + ++ ++E G V IN+ + SN Sbjct: 360 FGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASN 419 Query: 448 EVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481 PFGGIK SG GRE ++ GI++++ IK + LG Sbjct: 420 PYLPFGGIKKSGYGRELAENGIKEFMNIKTVYLG 453 Lambda K H 0.317 0.135 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: 511 Number of extensions: 22 Number of successful extensions: 2 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: 453 Length adjustment: 33 Effective length of query: 450 Effective length of database: 420 Effective search space: 189000 Effective search space used: 189000 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 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