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 Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::Q64057
         (539 letters)



>lcl|FitnessBrowser__Cola:Echvi_0535 Echvi_0535 NAD-dependent
           aldehyde dehydrogenases
          Length = 514

 Score =  516 bits (1328), Expect = e-150
 Identities = 268/503 (53%), Positives = 343/503 (68%), Gaps = 7/503 (1%)

Query: 42  LQDLGLREDNEGVFNGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAW 99
           LQDLGL E N+G + G      +GE +++Y P + + + +V+  + + YE+ + +A+KA+
Sbjct: 11  LQDLGLNEVNKGTWTGVEFIDIKGEWLSSYSPVDGKELGKVQMTTRESYEKVLDQAEKAF 70

Query: 100 NIWADIPAPKRGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAG 159
             W  +PAP+RGE+VR+IG  LR K  LLG+LVS EMGK   EG+GEVQE +D+CD+A G
Sbjct: 71  KAWRKVPAPQRGEVVRQIGIELRNKKSLLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVG 130

Query: 160 LSRMIGGPTLPSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKG 219
           LSR + G T+ SERP H + EQW+PLG+VG+I+AFNFPVAV+ WN  IA + G+VC+WK 
Sbjct: 131 LSRQLYGLTMHSERPSHRMYEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKP 190

Query: 220 APTTSLVSIAVTKIIAKVLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVG 279
           +  T L S+A   I A V   N  P  I SL  GGA++G  + +D RV L+S TGSTQ+G
Sbjct: 191 SEKTPLTSVACQLIAADVFNRNGFPEGITSLLIGGANVGAFLTQDPRVALISATGSTQMG 250

Query: 280 KQVALMVQERFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLH 339
           K V   V  R GK LLELGGNNAII  E ADL + +  ALF AVGTAGQRCT+ RRL +H
Sbjct: 251 KSVGETVGGRLGKVLLELGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIH 310

Query: 340 ESIHDEVVDRLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGG 399
           ES+ +EV +R+  AYS++ +GNP D + + GPL  K AV  ++ A+E  K EGG  V  G
Sbjct: 311 ESVFEEVKERMVAAYSKLTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAG 370

Query: 400 KVMDH----PGNYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGL 455
            +++      G YV P++     H   IV KETF PILY+ K+   +E     N V QGL
Sbjct: 371 GLLEGEEYVSGCYVRPSVFEAENH-FQIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGL 429

Query: 456 SSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQ 515
           SS+I T ++    R+L  +GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK 
Sbjct: 430 SSAIMTTNMREAERYLSSEGSDCGISNVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKA 489

Query: 516 YMRRSTCTINYSTALPLAQGIKF 538
           YMRR T TINYST LPLAQGIKF
Sbjct: 490 YMRRQTNTINYSTDLPLAQGIKF 512


Lambda     K      H
   0.319    0.137    0.417 

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: 849
Number of extensions: 46
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: 539
Length of database: 514
Length adjustment: 35
Effective length of query: 504
Effective length of database: 479
Effective search space:   241416
Effective search space used:   241416
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