Alignments for a candidate for adh in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Cereibacter sphaeroides ATCC 17029

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein

Query= reanno::Burk376:H281DRAFT_01117
         (795 letters)



>NCBI__GCF_000015985.1:WP_011842384.1
          Length = 791

 Score =  831 bits (2146), Expect = 0.0
 Identities = 445/799 (55%), Positives = 543/799 (67%), Gaps = 14/799 (1%)

Query: 1   MSVAEYFSSMDYGPAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAPASGER 60
           MS+ +   SMDYGPAPE    A+ WLA      GH+I GA+    + A  V + PA+GE 
Sbjct: 1   MSIKDIMESMDYGPAPEAATDAKAWLAARGHALGHYIDGAFTGAETAAIEVEN-PATGEI 59

Query: 61  LADIAQGDAADIDAALAAARAAQPGWLALGGKGRARHLYALARMVQRHSRLFAVLEALDN 120
           LA I     A+I+AA+AAARAA  GW  L G  RAR+LYA+AR +Q+  R F+VLE LDN
Sbjct: 60  LARIPAAGEAEIEAAVAAARAAFSGWSQLPGFERARYLYAIARGLQKRERFFSVLETLDN 119

Query: 121 GKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPLGVIGQIVPWNFPLLMLAWKIA 180
           GK IRETR  DVPL  RHF HHAGWA +   EF  H PLGV GQ++PWNFP+LMLAWKIA
Sbjct: 120 GKAIRETRTADVPLAIRHFYHHAGWAAVLGEEFPGHEPLGVCGQVIPWNFPMLMLAWKIA 179

Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVVTGDGSTGAALVEHPQVDKI 240
           PA+A GN VVLKPA+ TPLTA+ FAE+  + GLP GV+N+V G   TGA LV HP V K+
Sbjct: 180 PALAAGNTVVLKPADLTPLTAVAFAEMLDEIGLPRGVVNIVHGGAETGALLVRHPGVAKV 239

Query: 241 AFTGSTEVGKLIRSVTAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300
           AFTGST VG+ IR  TAGSGKSLTLELGGKSPF+V  DADLD AVEGVV+ +WFNQG+VC
Sbjct: 240 AFTGSTAVGREIRRATAGSGKSLTLELGGKSPFVVCADADLDAAVEGVVEGVWFNQGEVC 299

Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSIDMGAIVDPVQLERIHSLVETGRR 360
           CAGSRLL+QEGI  RF+AKL+ RME +RVG  LDKS DMGAIV   Q  RI  L+    R
Sbjct: 300 CAGSRLLLQEGIAERFLAKLRARMEKIRVGDPLDKSTDMGAIVSARQKARIEELIAGAAR 359

Query: 361 EGCAIWQAADTPLPANGCFYPPTLVTNVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420
           EG  + QAA  PLPA G F  P    +  PA+T+AQ EIFGP+ VT +FRT DEA+ALAN
Sbjct: 360 EGYRLEQAA-CPLPAAGHFVAPGFFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALAN 418

Query: 421 NSRYGLAASVWSETIGRALDVAPRLAAGVVWVNATNLFDAAVGFGGYRESGYGREGGREG 480
           N+ YGLAASVWSE I  A ++A R+ AGVVW+NA+NLFDA   FGG +ESG+GREG REG
Sbjct: 419 NTPYGLAASVWSENINAATELAARIRAGVVWINASNLFDAGASFGGMKESGFGREGAREG 478

Query: 481 IHEYLKPRAWLNLPKRQP---VSAATNASDDRQVSNLA-LVDRTAKLFIGGKQVRPDSGY 536
           +  YL+PR       R P   V+     +      NL+ L+DRT K +IGG QVRPD G 
Sbjct: 479 LGAYLRPRT-----PRGPEALVAPVDFTAHTGMGGNLSGLIDRTMKNYIGGAQVRPDGGA 533

Query: 537 SLPVHAPDGTRVGEVGEGNRKDIRNAVQAARAAQKWSQASTHNRAQVLFYLAENLAVRAD 596
           S  V  P G  +G      RKDIRNAV+AA  A+ W+ A+ H RAQVLF+LAEN+A RA+
Sbjct: 534 SYVVRGPKGEALGLAPVSGRKDIRNAVEAALKAKGWA-ANAHGRAQVLFFLAENIAARAE 592

Query: 597 EFAHQLTVRNGATDAAAHAEVEASVTRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGV 656
           + A  L V+ GA  + A AEV + + R+F YA  ADK DG +H    R + L++ EPLGV
Sbjct: 593 DLAAAL-VQGGAGRSEAAAEVRSLIERVFFYAGMADKDDGRIHATKPRHLTLSVKEPLGV 651

Query: 657 IGIACPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIV 716
           +G+  PDEAPLL+ +SL  P +A GNRVV +P  A  L      Q+ +TSD+PGGVVN+V
Sbjct: 652 VGVLAPDEAPLLSLMSLILPLIAAGNRVVAVPSPAQALLAQPLTQIFDTSDLPGGVVNLV 711

Query: 717 TGKREALLPALARHDDVDAVWCFGSAADATLIERESVGNLKRTFTDYGRQFDW-FDRASE 775
           TG R  L   LA HD VD +W  GSA  A  +E  S GNLK+ +T+ GR  DW  D  + 
Sbjct: 712 TGDRNLLARTLAEHDAVDGIWYHGSAKGAAEVEALSAGNLKQVWTNGGRALDWNADAVAC 771

Query: 776 GLPFLRQAVQVKNIWIPYG 794
           G  +L +A Q+K IW+PYG
Sbjct: 772 GRSWLDRATQIKTIWVPYG 790


Lambda     K      H
   0.320    0.135    0.411 

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: 1718
Number of extensions: 76
Number of successful extensions: 10
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: 795
Length of database: 791
Length adjustment: 41
Effective length of query: 754
Effective length of database: 750
Effective search space:   565500
Effective search space used:   565500
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: 55 (25.8 bits)

This GapMind analysis is from Apr 10 2024. 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