Alignments for a candidate for adh in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Marivita geojedonensis DPG-138

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_085639722.1 MGEO_RS15320 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_002115805.1:WP_085639722.1
          Length = 492

 Score =  538 bits (1386), Expect = e-157
 Identities = 270/488 (55%), Positives = 355/488 (72%), Gaps = 7/488 (1%)

Query: 36  VGGPADLHAD--LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVR 91
           V G  DL  D  +LR  +++ G W+     ATF V +PA G  +  VAD    E   A+ 
Sbjct: 5   VTGLKDLLKDPAILRTQAYIAGEWVDADDGATFSVSNPARGDTIAEVADVTRIETALAID 64

Query: 92  AAYDAFSSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFF 151
           AAY A   W + + KER+++LRKW+DLM++N D+LA I+TAE GKP  EA+GEILY A F
Sbjct: 65  AAYIAQKDWSKWTGKERAAVLRKWFDLMVENADDLATILTAEQGKPHAEARGEILYGASF 124

Query: 152 LEWFSEEARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGC 211
           +EWF+EEA+R YG+ I    +DKR  V+KQP+GVA+ ITPWNFP+AMITRKVG ALAAGC
Sbjct: 125 VEWFAEEAKRTYGETIPGHQRDKRITVIKQPIGVAASITPWNFPNAMITRKVGPALAAGC 184

Query: 212 TVVVKPAEDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFT 271
             V +PA +TP SALAL +LA +AGIP GV ++IP SR  + ++G+  C +P V K++FT
Sbjct: 185 AFVARPAAETPLSALALGELAERAGIPKGVLSIIPSSR--SSDIGKEFCENPKVRKLTFT 242

Query: 272 GSTATGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCS 331
           GST  G+ILL  AA+ V + SMELGG APFIVFD AN+D AV GA+ SK+RN GQTCVC+
Sbjct: 243 GSTEVGRILLKQAADQVMKCSMELGGNAPFIVFDDANLDAAVEGALISKYRNNGQTCVCA 302

Query: 332 NRFLVQRGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKG 391
           NR  VQ G++D+F  K  +A+ +++ VG+G  +G   GPLINE+AV KVE+HV DA+AKG
Sbjct: 303 NRIYVQAGVYDAFAAKLKDAV-EAMPVGDGLSDGVQLGPLINEEAVAKVEEHVEDAIAKG 361

Query: 392 ATVVTGGKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAAD 451
            TV++GGKRH  GG FF+PT+++  TR+M    EETFGP+AP+  FD  EE + +AN   
Sbjct: 362 GTVISGGKRHDLGGTFFQPTIVTGATREMAFAQEETFGPLAPLFNFDTVEEVIDLANDTI 421

Query: 452 VGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDE 511
            GLA YFY++D +++ +V E LE GMVGVN GLIS+   PFGGVKQSGLGREGS +G+DE
Sbjct: 422 FGLAAYFYARDLSRVTQVQEALEYGMVGVNTGLISTEVAPFGGVKQSGLGREGSHHGMDE 481

Query: 512 YLEVKYVC 519
           ++E+KY+C
Sbjct: 482 FMEMKYIC 489


Lambda     K      H
   0.318    0.135    0.400 

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: 680
Number of extensions: 35
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: 523
Length of database: 492
Length adjustment: 34
Effective length of query: 489
Effective length of database: 458
Effective search space:   223962
Effective search space used:   223962
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: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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 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