GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Acidovorax sp. GW101-3H11

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1496
          Length = 500

 Score =  292 bits (747), Expect = 2e-83
 Identities = 166/460 (36%), Positives = 255/460 (55%), Gaps = 8/460 (1%)

Query: 23  WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPE--WEALPAIERASWLRKISAGIR 80
           W+ V +PATE V++  PD  A D  +A+ +A+RA     W  L   +R   L ++S  I 
Sbjct: 38  WLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADREKLLFRLSELIE 97

Query: 81  ERASEISALIVEEGGKIQQLAE-VEVAFTADYIDYMAEWARRYEGEIIQSDRP--GENIL 137
             A E+SAL   + GK+Q +A  ++V   A+++ YMA WA + EG+ + +  P  G   +
Sbjct: 98  RHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTLDNSIPIPGPQWV 157

Query: 138 LFKRA--LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEI 195
            + R   +GV   I+PWNFP  +   K+APAL  G T+V+KPSE TP  A+  A +  E 
Sbjct: 158 TYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLTALRLAHLALEA 217

Query: 196 GLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGK 255
           G+P GV N+V GRG T G  L  +P V  +S TGS + G+ +   A +N+ +  LELGGK
Sbjct: 218 GIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHAAVENMARFTLELGGK 277

Query: 256 APAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFG 315
           +PA+VM+DAD     + I      + GQVC  + R+ V + +Y + ++ L    Q ++ G
Sbjct: 278 SPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLDELAGIAQGMRIG 337

Query: 316 NPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQ 375
           +  +      GPL + A   RV   +A A  EGA +  GG+ V   G +  PT+  D   
Sbjct: 338 SGFDA-ATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERVHDAGCFVQPTIFADTTA 396

Query: 376 EMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGET 435
           +M ++ EE FGPVL V  FD +EDAI+ AND+ YGL +S++TQ+L+ A + +  L+ G  
Sbjct: 397 QMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHAHRIVPRLQAGVV 456

Query: 436 YINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
           ++N  N         G ++SG G   G+  +  + + + V
Sbjct: 457 WVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496


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: 540
Number of extensions: 25
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: 500
Length adjustment: 34
Effective length of query: 445
Effective length of database: 466
Effective search space:   207370
Effective search space used:   207370
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 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