Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate CA265_RS05705 CA265_RS05705 aldehyde dehydrogenase (NADP(+))
Query= SwissProt::Q08IC0 (525 letters) >FitnessBrowser__Pedo557:CA265_RS05705 Length = 528 Score = 484 bits (1245), Expect = e-141 Identities = 257/518 (49%), Positives = 340/518 (65%), Gaps = 3/518 (0%) Query: 3 LTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQ 62 + G+ ++ + + + +L+A +P+ G +D F A++ V+ A A AF +YR Sbjct: 1 MNGQNIVASTYIEVNERSLKAVNPATGLTLDGDFFK-ASERLVDDALTSATLAFQSYRNL 59 Query: 63 PLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGR 122 +AAFL AIADEI LG+ L+ RA AE+GLP+ RLQGE GRT GQLRLFA +V +G Sbjct: 60 NKDLKAAFLNAIADEIANLGEELVNRASAESGLPLGRLQGELGRTTGQLRLFANLVAEGS 119 Query: 123 FLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPV 182 ++ A ID A P R PLPR D+R + +GPVVVFGASNFPLAFSVAGGDTASALA+GCPV Sbjct: 120 WVDAIIDTALPERQPLPRPDIRRMLIPIGPVVVFGASNFPLAFSVAGGDTASALASGCPV 179 Query: 183 IVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTG 242 +VKAH AH GTS LVG AI A KTGMP GVFSLL G IG LV HP +AV FTG Sbjct: 180 VVKAHPAHYGTSALVGGAIIKAAEKTGMPKGVFSLLYDDGYTIGAGLVQHPLTKAVTFTG 239 Query: 243 SRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQF 302 S +GGMAL+ +A R QPIPV+AEM SINPV+ P A+ + + +A + S+TLG GQF Sbjct: 240 SFKGGMALINLAQQREQPIPVFAEMGSINPVIFLPKAIENQAEELAKKYAASITLGAGQF 299 Query: 303 CTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIG 362 CTNPGL+LA+ P L+ F+ +A++ P+ MLT+GIA Y ++ GV + Sbjct: 300 CTNPGLLLAVQSPALESFKAALKEAISTIPSATMLTEGIASNYGKLSAEVVNEGGVALLS 359 Query: 363 AGEAAQTDC--QAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420 A T+ Q+ + +V A F+ P E+FGP SL+V +D+ E+ + ++ LEG Sbjct: 360 ASTVKNTELQNQSEAKIAQVSAADFIKNPKLREEIFGPYSLLVVAQDIAELEKAIDVLEG 419 Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480 QLT TL + + + L+ L K GR+++NG PTGVEVC AM HGGPFPAT++ T Sbjct: 420 QLTVTLMAEKQELQGYQTLVNKLTDKTGRIILNGVPTGVEVCAAMQHGGPFPATNDSRFT 479 Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPR 518 SVG+TAI RF RP+ YQD+ +LLP+ L++ NPL I R Sbjct: 480 SVGSTAINRFARPLAYQDWEQELLPDELKDGNPLGIFR 517 Lambda K H 0.320 0.137 0.396 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: 745 Number of extensions: 43 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: 525 Length of database: 528 Length adjustment: 35 Effective length of query: 490 Effective length of database: 493 Effective search space: 241570 Effective search space used: 241570 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 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