GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Pedobacter sp. GW460-11-11-14-LB5

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)



>lcl|FitnessBrowser__Pedo557:CA265_RS05705 CA265_RS05705 aldehyde
           dehydrogenase (NADP(+))
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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