Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= reanno::acidovorax_3H11:Ac3H11_612 (483 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 229 bits (584), Expect = 1e-64 Identities = 144/461 (31%), Positives = 237/461 (51%), Gaps = 17/461 (3%) Query: 27 STNPSDTREVVAEYARADRNQTELAVRAAADALPTWSQSTPQRRADVLDMIGSELLARKD 86 S NP T E++ E+ Q E A++ +A +W + +RAD++ G L D Sbjct: 3 SINPY-TGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTD 61 Query: 87 ELGALLAREEGKTLPEGVAEVARSGQIFKFFAGEALRIQGELLASVRQGVQVDVTREPVG 146 + G +++ E GK + E +EV + + +++A A + + ++ G + V P+G Sbjct: 62 KYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPLG 121 Query: 147 VVGIIAPWNFPFAIPAWKI----APALAYGNTVVFKPAELVPACGWALAEIISRSGLPAG 202 +V + PWNFPF W++ AP L GN + K A VP C A+ E+ +++G P G Sbjct: 122 IVLAVMPWNFPF----WQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEG 177 Query: 203 AF-NLIMGSGREVGQTLVDHPLVNALSFTGSVATGDRILRAASQRRAKVQLEMGGKNPLI 261 F +L++GS + ++ HP V A + TGS G +I A ++ K LE+GG +P I Sbjct: 178 VFQSLLIGSDKVAN--IIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFI 235 Query: 262 VLADADLDQAVDCALQGSYFSTGQRCTASSRLIVEAEVHDAFVARLRNRLASLKVGHALE 321 VL DAD+ +A A +G + GQ C A+ R I+E EV+D F+ ++ + S G L+ Sbjct: 236 VLKDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLD 295 Query: 322 RGTEMGPVVDDNQLAQNLGYIDIAKSEGAEHVWGGERLERPTPGHYMSP-ALFLARPEHR 380 + + + ++ + +GAE + G + E+ ++ P L P+ Sbjct: 296 EKAGYACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKA--FIKPYILGKLTPDMP 353 Query: 381 VAREEIFGPVACVLRADDYDHALALANDTPFGLCAGICTTSLKRAMHFKRHAAVGMTMVN 440 REE+FGPVA V +A+D D A+A+AND+ FGL A + T ++A R G +N Sbjct: 354 AYREELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFIN 413 Query: 441 LPTAGVDFHVPFGGRKESSYGAREQGRYAAEFYTTVKTGYM 481 A + ++PFGG K+S YG RE + + +KT Y+ Sbjct: 414 SMVAS-NPYLPFGGIKKSGYG-RELAENGIKEFMNIKTVYL 452 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: 429 Number of extensions: 13 Number of successful extensions: 5 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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