Aligments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::A1B4L2
         (508 letters)



>lcl|FitnessBrowser__Cola:Echvi_0481 Echvi_0481 NAD-dependent
           aldehyde dehydrogenases
          Length = 509

 Score =  699 bits (1805), Expect = 0.0
 Identities = 333/504 (66%), Positives = 399/504 (79%)

Query: 5   QTHPFRGVNALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELAL 64
           Q  P   ++   F+  YDNFIGG++V PV G YF   +P+ G    ++AR +A DIELAL
Sbjct: 6   QEKPATMLDRPDFKPHYDNFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELAL 65

Query: 65  DAAHAAKEKWGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAI 124
           DAAH A   W  TS  ER+NI+LKIADR+E  LE LA  ET DNGKP+RET+ ADL L +
Sbjct: 66  DAAHKAFPAWSRTSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVV 125

Query: 125 DHFRYFAGVLRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAG 184
           DHFRYFAGV+RA+EGSI+++D  TV+ +  EP+G+VGQIIPWNFP+LMA WK+APA+AAG
Sbjct: 126 DHFRYFAGVIRAEEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAG 185

Query: 185 NCVVLKPAEQTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGET 244
            C ++KPAEQTPA IM+   +IGDLLP GVLN+VNGFG EAGKPLA S R+ K+AFTGET
Sbjct: 186 CCTIVKPAEQTPASIMILMEVIGDLLPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGET 245

Query: 245 TTGRLIMQYASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCT 304
           TTGRLIMQYASENL PVT+ELGGKSPN+FF  V   DD+F DK LEG  MFALNQGEVCT
Sbjct: 246 TTGRLIMQYASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCT 305

Query: 305 CPSRVLIQESIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKE 364
           CPSR+L+ E IYD FME+ + R +AI+ G P +  TM+GAQAS +Q EKILSY+DIGK+E
Sbjct: 306 CPSRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQE 365

Query: 365 GAEVLTGGKAADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEI 424
           GAEVLTGG+ A L   L  GYY++PT+ +G+NKMR+FQEEIFGPV SV TFKD  EA+ I
Sbjct: 366 GAEVLTGGEVAKLNSGLENGYYVKPTLLKGHNKMRVFQEEIFGPVCSVATFKDVEEAISI 425

Query: 425 ANDTLYGLGAGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHK 484
           +NDTLYGLGAGVW+RDA+  Y++ R IKAGRVW NCYHAYPAHA FGGYK+SG GRETH 
Sbjct: 426 SNDTLYGLGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHL 485

Query: 485 MMLDHYQQTKNMLVSYSPKKLGFF 508
           MML+HY+Q KNML+SY   KLGFF
Sbjct: 486 MMLNHYRQNKNMLISYDKNKLGFF 509


Lambda     K      H
   0.319    0.136    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: 831
Number of extensions: 28
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: 508
Length of database: 509
Length adjustment: 34
Effective length of query: 474
Effective length of database: 475
Effective search space:   225150
Effective search space used:   225150
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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, or view the source code.

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