GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Acidithiobacillus ferrooxidans ATCC 23270

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_000021485.1:WP_012536996.1
          Length = 506

 Score =  345 bits (886), Expect = 2e-99
 Identities = 202/476 (42%), Positives = 280/476 (58%), Gaps = 17/476 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI   +V     + F  +SP   +   Q+  + +EDI+ A++AA AA   +W  +    R
Sbjct: 22  FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAA-KDAWGRTSVTAR 80

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L K+AD ID + + LA  E  DNGK++  +   DV L++ +FR  AG     +G++ 
Sbjct: 81  SNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEGTIG 140

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E  +    Y   EP+GV GQIIPWNFPLLMA WKL P L  G   VLK AE TP S L +
Sbjct: 141 EIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASILVM 200

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             LI +   P GV+NVV+G+G  AG  +++  +I K+AFTGST  G  IMK AAE N+  
Sbjct: 201 MELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAAE-NIIP 258

Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
            T+ELGGKSPNI F      +DA V   ++  V   F+N GEVC   SR+ +QE IY+K 
Sbjct: 259 STVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLA-FFNQGEVCTCPSRLLIQESIYEKF 317

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG--ERFGN 374
           +      +  +K G+P   +  +GAQ SQ Q DKIL YI IGK EGA VITGG  E    
Sbjct: 318 IGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGAVETMSA 377

Query: 375 ---KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431
              +GY+I+PT+      + ++ ++EIFGPVV++T FK   E +A+AND E+GL AGV T
Sbjct: 378 DYCEGYYIQPTLLKGTN-NMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWT 436

Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487
            +++ A  +   I +G +W N Y+ +     FGGY +SG+GRE  +  LD+Y Q K
Sbjct: 437 RDMNRAYRMGRGIQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTK 492


Lambda     K      H
   0.316    0.133    0.389 

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: 607
Number of extensions: 23
Number of successful extensions: 7
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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 (21.6 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