Alignments for a candidate for adh in Desulfuromusa kysingii DSM 7343

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Desulfuromusa kysingii DSM 7343

Align Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized)
to candidate WP_092346115.1 BLU87_RS07020 aldehyde dehydrogenase

Query= curated2:Q2YV11
         (495 letters)



>NCBI__GCF_900107645.1:WP_092346115.1
          Length = 491

 Score =  548 bits (1411), Expect = e-160
 Identities = 267/491 (54%), Positives = 359/491 (73%)

Query: 5   VRDYIAENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQEAFE 64
           +R+ I + Y L+I+G++V  S  +T E   PA G+ L+    A  +DVD AV+ A +AF 
Sbjct: 1   MRNQIDKQYKLYIDGKWVDASDGKTFEAHCPADGKLLATCANATKQDVDDAVKAAWKAFP 60

Query: 65  SWSLTSKSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFHYFAS 124
            W   S  +R+ +L  I D +    +K+AMIE+++NGKP+RETTA+D+P A+ HF YFA 
Sbjct: 61  EWKDISPQDRSIILLKIADLIDENAEKLAMIESIDNGKPLRETTAVDVPLASDHFRYFAG 120

Query: 125 VIETEEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIVIQPS 184
           VI  +EG    IDK+TMSI+  EPIGV+G ++ WNFP+L+AAWKIAPA+AAGN +V++PS
Sbjct: 121 VIRAQEGQAVMIDKNTMSIILREPIGVIGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPS 180

Query: 185 SSTPLSLLEVAKIFQEVLPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGYQVAE 244
           S+T LSLLE AK+   VLP GVVN++TGKGS +GN +  H+G  KL+FTGST+VGY +A+
Sbjct: 181 STTSLSLLEFAKLLDTVLPPGVVNVVTGKGSSTGNFVLEHEGFSKLAFTGSTEVGYNIAD 240

Query: 245 AAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHEKIYD 304
           AAAK L+PATLELGGKSANI  +D   + A+EG QLGIL NQG+VC AGSR+ V E IYD
Sbjct: 241 AAAKKLIPATLELGGKSANIYFEDCPWEKAIEGTQLGILLNQGQVCCAGSRVFVQESIYD 300

Query: 305 QLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDVAKESDAQILAGGHRLTE 364
           + V  + EAF  +KV  P  + T MG+Q  + QL+KI +Y++V K+  A+++ GG R+T 
Sbjct: 301 KFVEAMAEAFKKVKVNLPWADGTMMGAQIDEVQLNKILAYVEVGKQEGARLVTGGKRITT 360

Query: 365 NGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSKYGLAGGVF 424
             L KG+F EPTL A  +N  ++AQEEIFGPV+ VIK KD++E I++ANDS YGLAG V+
Sbjct: 361 GELGKGYFMEPTLFADVNNDMRIAQEEIFGPVVCVIKFKDEEEVINMANDSDYGLAGAVW 420

Query: 425 SQNITRALNIAKAVRTGRIWINTYNQVPEGAPFGGYKKSGIGRETYKGALSNYQQVKNIY 484
           +++I RAL +A+AV+TGR+W+NTYNQ+P   PFGGYKKSGIGRET+K  L +Y Q KNIY
Sbjct: 421 TKDINRALRVARAVQTGRMWVNTYNQLPAHTPFGGYKKSGIGRETHKMMLEHYTQTKNIY 480

Query: 485 IDTSNALKGLY 495
           I  +    GLY
Sbjct: 481 ISMTEDKIGLY 491


Lambda     K      H
   0.315    0.133    0.377 

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: 635
Number of extensions: 22
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: 495
Length of database: 491
Length adjustment: 34
Effective length of query: 461
Effective length of database: 457
Effective search space:   210677
Effective search space used:   210677
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. 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