GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sphingomonas koreensis DSMZ 15582

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  243 bits (619), Expect = 1e-68
 Identities = 152/455 (33%), Positives = 230/455 (50%), Gaps = 16/455 (3%)

Query: 26  VVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASE 85
           V++PAT    +  P     D   A+ AA RA P W A P  +RA+ +  I+  I     E
Sbjct: 21  VIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAIADSIEAAKDE 80

Query: 86  ISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEG-----EIIQSDRPGENILLFK 140
           ++ L+  E GK    A  E+            WAR   G     ++++ D     + + +
Sbjct: 81  LARLLSAEQGKPVPNAVGEIMGAL-------AWARATAGLRPAVDVLKDD-DSVRVEVHR 132

Query: 141 RALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRG 200
           + LGV   I PWNFP  +    + P L+ GNT+V+KPS FTP  A+   +I +   LP G
Sbjct: 133 KPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIANA-HLPPG 191

Query: 201 VFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIV 260
           V N V G  E +G+ +A +P +  +  TGS   G  IMA  A N+ ++ LELGG   AIV
Sbjct: 192 VLNSVTGEVE-IGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGNDAAIV 250

Query: 261 MDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAER 320
           + DAD++     I      NSGQ+C   +RVYV + I+D    +L E  +    G P   
Sbjct: 251 LPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVG-PGSD 309

Query: 321 NDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIM 380
                GP+ N    + V      A   G R   GG+A EG GY++P ++++DV   M I+
Sbjct: 310 AASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVVDVTDGMRIV 369

Query: 381 HEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRE 440
            EE FGP+LPV+ +   EDA++ AN ++ GL  S+++ +   A+   + L+ G  ++N  
Sbjct: 370 DEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVNDH 429

Query: 441 NFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
              +      G ++SG+G   G +GL EY+Q Q V
Sbjct: 430 ASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTV 464


Lambda     K      H
   0.318    0.135    0.392 

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: 583
Number of extensions: 27
Number of successful extensions: 5
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: 479
Length of database: 469
Length adjustment: 33
Effective length of query: 446
Effective length of database: 436
Effective search space:   194456
Effective search space used:   194456
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: 51 (24.3 bits)

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

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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:

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