Alignments for a candidate for davD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Cupriavidus basilensis 4G11

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate RR42_RS26155 RR42_RS26155 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Cup4G11:RR42_RS26155
          Length = 487

 Score =  654 bits (1688), Expect = 0.0
 Identities = 316/480 (65%), Positives = 393/480 (81%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           + L+   L R    +DG W  A  G  + V+NPAT +++G+VP+ GAAETR+A+EAA +A
Sbjct: 5   LTLQRPGLLRSACLIDGEWTGAAGGAVLMVHNPATHDVVGTVPRCGAAETRQAVEAAARA 64

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
           LPAWR LT K RA  LRRW DLM+ +Q+DLA+LMT EQGKPLAEA+GEIAYAASFLEWFG
Sbjct: 65  LPAWRDLTGKARAAVLRRWADLMLVHQEDLAQLMTAEQGKPLAEARGEIAYAASFLEWFG 124

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EEAKR+ GD +   +  ++++V++QP+GV AAITPWNFP+AMITRKAGPALAAGCTM++K
Sbjct: 125 EEAKRVDGDVLSSPRAGQKMLVLRQPVGVCAAITPWNFPAAMITRKAGPALAAGCTMIVK 184

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           PA QTP +ALALA LAE AG+P+GV  VVTG   ++GG L  +P+VRKL+FTGST IG+ 
Sbjct: 185 PAEQTPLTALALAALAEEAGVPRGVLQVVTGDPVQIGGVLCESPVVRKLSFTGSTAIGKL 244

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           LMA+CA  +KK+SLELGGNAP IVF+DADLD AV+G L SK+RN+GQTCVCANR+YV D 
Sbjct: 245 LMAQCAGTVKKLSLELGGNAPLIVFEDADLDRAVDGILASKFRNSGQTCVCANRIYVHDA 304

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYD    +L  AV+ L  G+G+++ VT GPLIDA AVAKVE HIADA++ GA+V++GGK 
Sbjct: 305 VYDEVASRLVRAVSALRPGHGIDSDVTQGPLIDADAVAKVESHIADALAHGARVLTGGKR 364

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           HALGGTFFEPT++        V+++ETFGPLAP+FRFK + EVIAM+NDTE GLA+YF++
Sbjct: 365 HALGGTFFEPTVVAGATAAMRVAREETFGPLAPLFRFKGDQEVIAMANDTESGLAAYFFS 424

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           +D+ARV+RVAE LEYGMVGINTGLISNEVAPFGG+K SGLGREGS YGI++YLE+KYLCL
Sbjct: 425 KDMARVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSSYGIDEYLEMKYLCL 484


Lambda     K      H
   0.317    0.135    0.391 

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: 676
Number of extensions: 12
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: 483
Length of database: 487
Length adjustment: 34
Effective length of query: 449
Effective length of database: 453
Effective search space:   203397
Effective search space used:   203397
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: 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)
Rules (tab-delimited)
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