Alignments for a candidate for adh in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Synechococcus elongatus PCC 7942

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase

Query= curated2:P39616
         (456 letters)



>FitnessBrowser__SynE:Synpcc7942_0489
          Length = 459

 Score =  425 bits (1093), Expect = e-123
 Identities = 215/443 (48%), Positives = 289/443 (65%)

Query: 12  KAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIGIVLEEI 71
           +A F  G TR L  RL  L+ L + V  +EA+L+ AL  DL K   EAY++EI  V ++I
Sbjct: 17  QATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQI 76

Query: 72  SFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPLIGAIAA 131
               K LR+W +P++    L     ++    EP G VL+I PWNYP QL ++PLIGAIAA
Sbjct: 77  KLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAIAA 136

Query: 132 GNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIFFTGSVA 191
           GN  VLKPSE  PA S+++ +LIS  F  DY+ + EG   VS AL+ QPFD+IFFTG  A
Sbjct: 137 GNCAVLKPSELAPATSSLIQRLISDRFDPDYIRVLEGDASVSQALITQPFDHIFFTGGTA 196

Query: 192 VGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCIAPDYLF 251
           +G+ VM AAA+ L PVTLELGGKSPCIV  D D+ +AA+RI +GKF NAGQTCIAPDYL 
Sbjct: 197 IGRKVMAAAAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLL 256

Query: 252 VHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLTGGQSDP 311
           V   +     E +   I++FYG  P+++  Y +IVS+RH+QRL S L DG    GGQ D 
Sbjct: 257 VQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLLVDGTIRHGGQVDR 316

Query: 312 NHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLALYLFTTNK 371
           +   IAPT++  V    P++QEEIFGP+LP+  Y  + E I +++++PKPLALYLF+ ++
Sbjct: 317 SDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDR 376

Query: 372 EIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFTHKKSVVKQ 431
           +++  VL   S G  C+NDT++ V  P   FGGVG SG+G YHG  SF TF+H K V+K+
Sbjct: 377 QVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLVLKR 436

Query: 432 TNRFDFAFRYPSSKNGLRMIRKI 454
               D A RYP   + + + RK+
Sbjct: 437 PFWLDLALRYPPYGDKINLFRKL 459


Lambda     K      H
   0.320    0.137    0.401 

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: 565
Number of extensions: 13
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: 456
Length of database: 459
Length adjustment: 33
Effective length of query: 423
Effective length of database: 426
Effective search space:   180198
Effective search space used:   180198
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: 51 (24.3 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