GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Acidithiobacillus ferrooxidans ATCC 23270

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  248 bits (633), Expect = 3e-70
 Identities = 160/478 (33%), Positives = 249/478 (52%), Gaps = 21/478 (4%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +I G++V      + DV+ P      ++     AED   A+DAA     +W      ERA
Sbjct: 22  FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81

Query: 70  SWLRKISAGIRERASEIS-ALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
           + L K++  I      ++ A  V+ G  I++    ++    D+  Y A   R  EG I  
Sbjct: 82  NILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGGISD 141

Query: 129 SDRPGENILL--FKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186
            D   EN +   F   LGV   I+PWNFP  + + K+APAL  GN +V+KP+E TP + +
Sbjct: 142 ID---ENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISIL 198

Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNIT 246
             A+++ ++ LP GV N+V G G   G  LA + ++A ++ TGS + G  I   AA ++ 
Sbjct: 199 ILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLI 257

Query: 247 KVCLELGGKAPAIVM------DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300
              LELGGK+P I        DD+ L+ A++ +V     N G+VC C  R  +Q+ IYD+
Sbjct: 258 PATLELGGKSPNIFFADVMDKDDSFLDKAIEGLV-LFAFNQGEVCTCPSRALIQESIYDK 316

Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKA--V 358
           F+ R  + ++A++ GNP + N + +G   +   L ++   +    +EGA+V  GG    V
Sbjct: 317 FMERCLDRIKAIKQGNPLDTNTM-IGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAIV 375

Query: 359 EGK---GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSI 415
           +G    GYY  PTL      +M I  EE FGPVL V  F    +A+S+AND+ YGL + +
Sbjct: 376 DGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGV 434

Query: 416 YTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473
           +++N NVA +  + +K G  +IN  +         G+++SGIG    K  L  Y QT+
Sbjct: 435 WSRNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTK 492


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: 551
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: 506
Length adjustment: 34
Effective length of query: 445
Effective length of database: 472
Effective search space:   210040
Effective search space used:   210040
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 Apr 09 2024. 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