GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pedobacter sp. GW460-11-11-14-LB5

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Pedo557:CA265_RS24850
          Length = 454

 Score =  238 bits (607), Expect = 3e-67
 Identities = 141/456 (30%), Positives = 231/456 (50%), Gaps = 4/456 (0%)

Query: 24  IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83
           + ++NPAT  +I+ + +      +   DA ++AQP+W      ER + +   S  +    
Sbjct: 1   MQIINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEI 60

Query: 84  SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRAL 143
            ++++++  E GK  Q +  E+      I +M   A +Y  + + +D PG   ++    L
Sbjct: 61  EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL 120

Query: 144 GVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFN 203
           GV   I  WN+P+ +      PALL+GNT++ KPSE+     I   K++ + G+P  VF+
Sbjct: 121 GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH 180

Query: 204 LVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263
           + +G  ET    L  N        TGS   G+ I    A  +    LELGGK P  + DD
Sbjct: 181 IAIGAKETGSALL--NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDD 238

Query: 264 -ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERND 322
             D+  A     D    N+GQ C   ER+YVQ+  YD + N     +++ + G P     
Sbjct: 239 VTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEG- 297

Query: 323 IAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHE 382
           + +G L     +  +E +V  A+ +GA++  GGKAVEGKGYY+ PT+L DV  +M +M E
Sbjct: 298 VYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQE 357

Query: 383 ETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENF 442
           E+FGP++ ++      +A+ M  D+DYGLT+S+YT +   A K +  L  G  Y N  + 
Sbjct: 358 ESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDR 417

Query: 443 EAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478
            +     +G + SGIG      G+  + + +  +L+
Sbjct: 418 VSAALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLR 453


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: 489
Number of extensions: 17
Number of successful extensions: 4
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: 454
Length adjustment: 33
Effective length of query: 446
Effective length of database: 421
Effective search space:   187766
Effective search space used:   187766
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