GapMind for catabolism of small carbon sources

 

Alignments 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)



>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.

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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:

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