GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_0535
          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.

Links

Downloads

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:

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:

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:

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:

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