Alignments for a candidate for adh in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Pedobacter sp. GW460-11-11-14-LB5

Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate CA265_RS21385 CA265_RS21385 aldehyde dehydrogenase family protein

Query= SwissProt::P12693
         (483 letters)



>FitnessBrowser__Pedo557:CA265_RS21385
          Length = 465

 Score =  410 bits (1054), Expect = e-119
 Identities = 215/451 (47%), Positives = 286/451 (63%), Gaps = 4/451 (0%)

Query: 22  VFNLQKVASSARRGKFGIAERIAALNLLKETIQRREPEIIAALAADFRKPASEVKLTEIF 81
           VF+LQ+      R K     RI  L LLK+ +++ E EI AAL AD RK   E  +TE+F
Sbjct: 8   VFDLQQKHKFELR-KTDAKTRIGKLKLLKQALEKAEEEIYAALEADLRKNRFETAVTELF 66

Query: 82  PVLQEINHAKRNLKDWMKPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPL 141
               EI+HA + L+ WMKP+ V   +S       + YEPKGVCLIIAPWNYP  L   PL
Sbjct: 67  FTYAEIDHAIKKLQGWMKPKSVARTMSNLFASNKIYYEPKGVCLIIAPWNYPLQLIMSPL 126

Query: 142 VSALAAGNSVVIKPSELTPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIF 201
           VSA+AAGN V++KPSEL+  TA +I  ++   F  + +A  EGDA VS  LL LPFDHIF
Sbjct: 127 VSAIAAGNCVILKPSELSAATADVISKLISNTFEAEEIACFEGDAEVSTALLKLPFDHIF 186

Query: 202 FTGSPRVGKLVMEAASKTLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCI 261
           FTGS  +GK+VMEAA+K L SVTLELGGKSP I+  T +L KAA  I WGK  N GQTCI
Sbjct: 187 FTGSTAIGKVVMEAAAKNLTSVTLELGGKSPAIVDETCDLKKAAEKIAWGKLVNAGQTCI 246

Query: 262 APDHVFVHRCIAQKFNEILVKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAK 321
           APD+V +   I+  F       + +++  + A  +   DY +I+N + F R+NKL+ +A 
Sbjct: 247 APDYVLIKENISADFEMYYQAAVQKMFFNEAAINKN--DYAKIINIKQFQRLNKLIEEAI 304

Query: 322 AKGAKILQGGQVDATERLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVND 381
             GA +  GG+ D     + PT+L++V  +  I  EEIFGP+LP+I Y ++   I  VN 
Sbjct: 305 RDGAVLAFGGKSDEQNLTITPTLLTSVAESSAIMQEEIFGPVLPVITYQNLQEAIDVVNR 364

Query: 382 GDKPLALYVFSEDKQFVNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVY 441
             KPLALY+FS+     N I++ TS+G   VN  +VH  +P+LPFGGVNNSGIGS HG++
Sbjct: 365 KAKPLALYIFSDSTTNQNKIISETSAGGTCVNDVLVHIGNPDLPFGGVNNSGIGSCHGIF 424

Query: 442 GFRAFSHEKPVLI-DKFSITHWLFPPYTKKV 471
           GF+ FSHE+ V+   K  +T  ++PPY  K+
Sbjct: 425 GFKTFSHERAVVFQSKLDLTKMIYPPYASKM 455


Lambda     K      H
   0.320    0.136    0.395 

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: 512
Number of extensions: 15
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: 483
Length of database: 465
Length adjustment: 33
Effective length of query: 450
Effective length of database: 432
Effective search space:   194400
Effective search space used:   194400
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
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