Alignments for a candidate for dopDH in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Cupriavidus basilensis 4G11

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate RR42_RS04830 RR42_RS04830 2,5-dioxovalerate dehydrogenase

Query= SwissProt::Q08IC0
         (525 letters)



>FitnessBrowser__Cup4G11:RR42_RS04830
          Length = 525

 Score =  644 bits (1662), Expect = 0.0
 Identities = 341/523 (65%), Positives = 397/523 (75%), Gaps = 2/523 (0%)

Query: 1   MQLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYR 60
           M +TGEMLIGA AV G+   L A +P+ GE + AP F     A+ ERAC LA  AFD YR
Sbjct: 1   MTITGEMLIGASAVRGTTKILHATNPATGEVL-APEFHGGGAAEAERACALAEAAFDTYR 59

Query: 61  AQPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRD 120
                 RA FLE+IA  + ALGD LIERAHAE+ LPVARLQGER RT GQLRLFA V+RD
Sbjct: 60  NTSPETRARFLESIASGLEALGDTLIERAHAESALPVARLQGERARTAGQLRLFASVLRD 119

Query: 121 GRFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGC 180
           GR+ +A++D A P RTP PR DLRLQK+ +GPV VFGASNFPLAFSVAGGDTASALAAGC
Sbjct: 120 GRWQSATLDSALPERTP-PRPDLRLQKIAVGPVAVFGASNFPLAFSVAGGDTASALAAGC 178

Query: 181 PVIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGF 240
           PV+VKAH AHLGTSELVGR I+ AVA  G+P GVFSLLVG G  +G ALV+HP++QAVGF
Sbjct: 179 PVVVKAHSAHLGTSELVGRVIQKAVADAGLPEGVFSLLVGAGVAVGTALVAHPSIQAVGF 238

Query: 241 TGSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVG 300
           TGSR GG+ALVQ AN+RPQPIPVYAEMSSINPV L PAALAARG  IA   VDSL +GVG
Sbjct: 239 TGSRSGGLALVQTANSRPQPIPVYAEMSSINPVFLLPAALAARGAQIARNLVDSLVMGVG 298

Query: 301 QFCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVRE 360
           QFCTNPGL+LA++ P LD F   A  ALA+K A  MLT GI+ AY NG  +L+++ G+R 
Sbjct: 299 QFCTNPGLLLAVESPALDVFRQGAIAALAEKAAATMLTPGISQAYDNGVAQLSDIEGLRR 358

Query: 361 IGAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420
           IG+G+ A    QA  AL+E  A+ FLA+     EVFGP+S++V CRD +E+  V   LEG
Sbjct: 359 IGSGQTASGPNQARPALFETTAERFLADHRMEAEVFGPSSVLVVCRDHEEMLAVARRLEG 418

Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480
           QLTAT+Q DA D+  A  LL VLERKAGR+L NGYPTGVEV  AMVHGGPFPATS+   T
Sbjct: 419 QLTATVQADAGDRAEAGSLLTVLERKAGRVLFNGYPTGVEVSYAMVHGGPFPATSDTRAT 478

Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523
           SVGA+AIERFLRPVCYQ+ P +LLP  LQ+ NPL + RL DG+
Sbjct: 479 SVGASAIERFLRPVCYQNVPAELLPPALQDGNPLKVWRLTDGQ 521


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: 908
Number of extensions: 42
Number of successful extensions: 3
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: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources