GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Burkholderia phytofirmans PsJN

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate BPHYT_RS24140 BPHYT_RS24140 2,5-dioxovalerate dehydrogenase

Query= SwissProt::Q08IC0
         (525 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS24140 BPHYT_RS24140
           2,5-dioxovalerate dehydrogenase
          Length = 527

 Score =  650 bits (1678), Expect = 0.0
 Identities = 333/523 (63%), Positives = 396/523 (75%)

Query: 1   MQLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYR 60
           M +TGEMLIG +AV G    L AF+P+ G  I  PVFG  + A V +ACELA+ AFD YR
Sbjct: 1   MTITGEMLIGRKAVRGEEKPLHAFNPATGSDIAEPVFGSGSVALVGQACELAQQAFDPYR 60

Query: 61  AQPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRD 120
             PL+ RA FLE IAD I ALGDALIERAH E+GLP ARL+GERGRT GQL+LFA+VVR 
Sbjct: 61  QLPLSVRAEFLERIADGITALGDALIERAHQESGLPKARLEGERGRTTGQLKLFAQVVRA 120

Query: 121 GRFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGC 180
           G++LAA++D   P R PLPRSDLR++K+ LGPV VFGASNFPLAFSVAGGDTA+ALAAGC
Sbjct: 121 GQWLAATLDSPLPERKPLPRSDLRMRKIPLGPVAVFGASNFPLAFSVAGGDTAAALAAGC 180

Query: 181 PVIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGF 240
           PV+VKAH AHLGTSE+VGR I+    +  +P GVFS++VG G  +G ALV+HPA++AVGF
Sbjct: 181 PVVVKAHRAHLGTSEMVGRVIQRVAQEMDLPEGVFSMIVGAGNSVGEALVAHPAIKAVGF 240

Query: 241 TGSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVG 300
           TGSR GG +L+++A AR +PIPVYAEMSSINPV L   ALAARG++IA GFVDSL LG G
Sbjct: 241 TGSRAGGTSLMRVAAARAEPIPVYAEMSSINPVFLLSNALAARGESIARGFVDSLVLGAG 300

Query: 301 QFCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVRE 360
           QFCTNPGL +A+D   L  F   A++AL+ KPA  MLT GI  AY  G GKLA + GV  
Sbjct: 301 QFCTNPGLAIAVDSDALKTFVATASEALSGKPAQTMLTSGICAAYEEGEGKLAAIKGVEA 360

Query: 361 IGAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420
           +  G       QA  AL+   AQ FLA PA   EVFGPAS IVRC+D  E+  V E  +G
Sbjct: 361 VARGVDTTGPTQARAALFVTDAQTFLATPALEDEVFGPASTIVRCKDEQELLAVAEYFDG 420

Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480
           QLTAT+QMD+ D   A++L+P+LERKAGR+LVNG+PTGVEV  AMVHGGPFPATS+   T
Sbjct: 421 QLTATVQMDSADLASAKKLVPILERKAGRILVNGFPTGVEVSHAMVHGGPFPATSDSRAT 480

Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523
           SVG T+IERFLRPVCYQDFP DLLPE L ++NPL + R RDG+
Sbjct: 481 SVGTTSIERFLRPVCYQDFPADLLPEALADNNPLDLWRRRDGE 523


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: 937
Number of extensions: 39
Number of successful extensions: 1
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: 527
Length adjustment: 35
Effective length of query: 490
Effective length of database: 492
Effective search space:   241080
Effective search space used:   241080
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 preprint 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