Aligments for a candidate for adh in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Cupriavidus basilensis 4G11

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate RR42_RS25005 RR42_RS25005 betaine-aldehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>FitnessBrowser__Cup4G11:RR42_RS25005
          Length = 495

 Score =  453 bits (1166), Expect = e-132
 Identities = 236/500 (47%), Positives = 327/500 (65%), Gaps = 11/500 (2%)

Query: 1   MSSLTMQVTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVD 60
           MSS T  V  +   F+ GTK+L+I G +VP+ASG  FDT NPATGE +  L +A   D+D
Sbjct: 1   MSSTTYGV--QTPAFVGGTKRLFIGGAWVPAASGKAFDTVNPATGEVIARLAQADQTDID 58

Query: 61  KAVKAARKAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGD 120
           +AV AAR+AF+ G W   + + R RL+ ++ D++E+H  ELA +ETLD G P+  T  G 
Sbjct: 59  RAVTAARQAFE-GPWNQWTHSDRQRLLIRIHDVVEKHFDELALIETLDMGAPLVRT-RGL 116

Query: 121 IPLAIEHMRYYAGWCTKITGQTIPVS---GAYFNYTRHEPVGVVGQIIPWNFPLLMAMWK 177
               ++ + +YA   T   G   P++   G +       PVGVV  IIPWN PLL   W 
Sbjct: 117 KSFLLQLILFYASQ-TAAGGVQTPLNALPGKFATLKIKAPVGVVAGIIPWNGPLLSQWWI 175

Query: 178 MGAALATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAV 237
           +GA LATGCT VLKPAE   LSAL +AEL+ +AG PAGVIN++ G+G +AG AL  H  V
Sbjct: 176 LGATLATGCTAVLKPAEDASLSALRMAELLQEAGVPAGVINVVTGYGGEAGSALAEHPGV 235

Query: 238 DKIAFTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQG 297
           D+IAFTGS E G++I+  +A + KRV++ELGGKSP+I+  DANL KA+PG   GV  N G
Sbjct: 236 DRIAFTGSPETGRRIVRASAGNFKRVSVELGGKSPDIVFDDANLDKAVPGVAMGVFTNTG 295

Query: 298 QVCCAGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQK 357
           Q+C AG+RV + +  YDE ++ + +++ SL+ G GL    Q+GP+VS+ Q +RV+ Y+  
Sbjct: 296 QICAAGTRVLVQRRIYDEFIERLKAFSTSLKIGNGLDPQVQLGPIVSQRQLDRVMHYVDV 355

Query: 358 GKDEGAKAVTGG---SCPFEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEV 414
           G  EGA+   GG        AGYFV PTVF  V ++MTIA+EEIFGPV + +P++T ++ 
Sbjct: 356 GGQEGAELACGGRRLGGELAAGYFVEPTVFTGVHNDMTIAREEIFGPVASVMPFDTPEQA 415

Query: 415 IERANHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGRE 474
           +  AN + +GLA G+WT+N+  AH  A  +QAGT+WVNCY V D    FGGYK SG G +
Sbjct: 416 LRIANDTSFGLAGGVWTQNLSTAHRFAQGIQAGTIWVNCYGVLDPQVGFGGYKLSGYGWK 475

Query: 475 MGSYALDNYTEVKSVWVNLE 494
             +  +D+Y   K+V++NL+
Sbjct: 476 GAAEQVDSYLYQKAVYMNLD 495


Lambda     K      H
   0.316    0.133    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: 654
Number of extensions: 25
Number of successful extensions: 4
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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 (21.6 bits)
S2: 52 (24.6 bits)

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

Downloads

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

Related tools

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