Alignments for a candidate for dgoD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Cupriavidus basilensis 4G11

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate RR42_RS31070 RR42_RS31070 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Cup4G11:RR42_RS31070
          Length = 576

 Score =  488 bits (1255), Expect = e-142
 Identities = 266/555 (47%), Positives = 347/555 (62%), Gaps = 4/555 (0%)

Query: 17  YGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWE 76
           YG     +   + ++K  GY  D    RPVIGI+NT S   PC+G+  +L E VK GV  
Sbjct: 16  YGDKGFSLFLRKAFIKGAGYTDDALS-RPVIGIVNTNSSYNPCHGNAPQLVEAVKRGVML 74

Query: 77  AGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLM 136
           AGG P++ P  S  E+   PT+M  RNL ++  EE IR QPMD  VL+ GCDKT P+ LM
Sbjct: 75  AGGLPVDFPTISVHESFSAPTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQLM 134

Query: 137 GAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRS 196
           GAAS  +P+I +  G ML G  RGERVG+ T   ++    +A E+   E  +    +  S
Sbjct: 135 GAASAGVPAIQLVTGSMLTGSHRGERVGACTDCRRYWGRYRAEEIDAPEIADVNNQLVAS 194

Query: 197 SGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSE 256
            GTC+ MGTASTMA + EALGM ++G A+ P V + R  +A+ TG   V M +  L P  
Sbjct: 195 VGTCSVMGTASTMACLTEALGMMVAGGASAPAVTADRVRVAERTGTTAVAMARSGLTPER 254

Query: 257 IMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSG 316
           I+T +A ENAIR   AIGGSTN ++HL AIAGR+GI + L   DR  R+ P +V+L PSG
Sbjct: 255 ILTGRAIENAIRVLLAIGGSTNGIVHLTAIAGRLGIGIDLAGLDRMSRETPVLVDLKPSG 314

Query: 317 KYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDV-VNWNEDVILPAEKA 375
           ++ ME+F  AGG+P +L+ L    LLH D LTVSG T+ +E+      + ++VI P +  
Sbjct: 315 QHYMEDFHAAGGMPALLREL--RPLLHLDTLTVSGRTLGEELDAAPAPFAQEVIRPFDAP 372

Query: 376 LTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDEN 435
           +   GG+ VLRGNLAP GA++K SAA P L+ H+GRAVVFED +D   +I+DD LD+  +
Sbjct: 373 IYPVGGLAVLRGNLAPGGAIIKQSAADPVLMEHEGRAVVFEDAEDMALRIDDDALDVKAD 432

Query: 436 CIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHTSPEA 495
            I+V+K  GP G PGM E G M +P K+ + G+ DMVRISD RMSGTA GT+VLH +PEA
Sbjct: 433 DILVLKRIGPTGAPGMPEAGYMPIPRKLARAGVKDMVRISDGRMSGTAAGTIVLHVTPEA 492

Query: 496 AVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVE 555
           A+GGPLA V+NGD I L V  R + L I D ELARR AE +        GY  L    V 
Sbjct: 493 AIGGPLAHVRNGDRIRLSVARREISLLIDDAELARRAAEHEVVRPAAERGYRKLFLATVT 552

Query: 556 GADTGADLDFLKGCR 570
            AD G D DFL+  R
Sbjct: 553 QADQGVDFDFLRAAR 567


Lambda     K      H
   0.318    0.135    0.408 

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: 943
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: 579
Length of database: 576
Length adjustment: 36
Effective length of query: 543
Effective length of database: 540
Effective search space:   293220
Effective search space used:   293220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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