Alignments for a candidate for adh in Bacillus altitudinis 41KF2b

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Bacillus altitudinis 41KF2b

Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate WP_008343682.1 BA79_RS18445 aldehyde dehydrogenase family protein

Query= curated2:Q49Z69
         (475 letters)



>NCBI__GCF_000691145.1:WP_008343682.1
          Length = 475

 Score =  592 bits (1527), Expect = e-174
 Identities = 293/472 (62%), Positives = 360/472 (76%), Gaps = 1/472 (0%)

Query: 1   MRNFTKQYINGEWVESTSGETLEVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRH 60
           MRN  K +INGEWV ST  ET EVINPATEEV GTI+ G KED++KAV+AA   +  F  
Sbjct: 1   MRNQEKHFINGEWVASTGNETTEVINPATEEVIGTISLGTKEDLDKAVKAARAAFPSFSK 60

Query: 61  TSVKERQDLLDQIVQEYKNRKEDLIQAITDELGAPLSVAENVHYQMGLDHFEAARDALND 120
           TS  ER ++L+ IV+ Y+ RK++L++ +T ELGAPL V+E VHY+MG +HF  A +AL  
Sbjct: 61  TSRNERVEMLENIVRGYEKRKDELVEVMTKELGAPLKVSEEVHYKMGYEHFSKAAEALKS 120

Query: 121 FQFEERRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAAI 180
           + F E RG   ++KEAIGVSGLITPWNFPTNQTSLK+A A AAGSPVV KP+E TPFAA+
Sbjct: 121 YTFTEDRGGHTIIKEAIGVSGLITPWNFPTNQTSLKIAGAIAAGSPVVLKPAEITPFAAM 180

Query: 181 ILAEIFDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDFK 240
           ILAEI D+ GVPKGVFNLVNG G  +G+ +S HP +  +SFTGSG  GS IM+ AA++ K
Sbjct: 181 ILAEIIDEAGVPKGVFNLVNGTGDVIGDGISSHPDIDFVSFTGSGAVGSKIMENAADNVK 240

Query: 241 KVSLELGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAVK 300
           KV+LELGGKSP I+LDDAD+D AA  A + +  NTGQVC+A TR ++P S+K+ F  A+ 
Sbjct: 241 KVALELGGKSPLIVLDDADVDEAAETAIHHIAMNTGQVCSAATRVLIPESMKDKFEKALL 300

Query: 301 EKFSQVKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGYF 360
               +  VG+PRE+    GP++SKKQ+D VQ+YI+KGIEEGA LL GG GKP+G+DKGYF
Sbjct: 301 NALPKFTVGDPREDHA-TGPLVSKKQWDTVQSYIEKGIEEGATLLAGGTGKPDGIDKGYF 359

Query: 361 ARPTIFNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTLH 420
           A+ TIF NV N MTIAQEEIFGPVMSVITY DLD A++IANDT YGLAGYV G D+ TL 
Sbjct: 360 AKHTIFTNVKNDMTIAQEEIFGPVMSVITYQDLDHALEIANDTVYGLAGYVVGQDEKTLK 419

Query: 421 KVARSIEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSIAG 472
            VA  I AG + IN A      PFGG+KQSG+GREWGD+GIEE+LEVK++ G
Sbjct: 420 YVAEHIRAGQITINNAETDYFAPFGGFKQSGIGREWGDFGIEEYLEVKAVMG 471


Lambda     K      H
   0.313    0.134    0.380 

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: 711
Number of extensions: 30
Number of successful extensions: 2
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: 475
Length of database: 475
Length adjustment: 33
Effective length of query: 442
Effective length of database: 442
Effective search space:   195364
Effective search space used:   195364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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