GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Acidithiobacillus ferrooxidans ATCC 23270

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000021485.1:WP_012536996.1
          Length = 506

 Score =  304 bits (779), Expect = 4e-87
 Identities = 175/470 (37%), Positives = 260/470 (55%), Gaps = 15/470 (3%)

Query: 16  GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75
           GE     +P  G    +I  +SAE ++ A+ AA AA   WG+T+   R+  LLK+AD I+
Sbjct: 33  GEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAAKDAWGRTSVTARSNILLKIADRID 92

Query: 76  ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135
            N ++ A  E+ + GK +    N ++P   D FR+FAG  R   G   GE  E   +   
Sbjct: 93  ANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEG-TIGEIDENTVAYHF 151

Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAG 195
            +PLGVV  I PWN+PL+MA WKLAPALAAGNCVVLKP+E TP + L + EL  D+ PAG
Sbjct: 152 HEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASILVMMELIADLLPAG 211

Query: 196 VINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIV 255
           V+N++ G G   G  L    ++  ++ TGS   G  I+ + A +I  + +ELGGK+P I 
Sbjct: 212 VLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAAENIIPSTVELGGKSPNIF 271

Query: 256 F------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKS 309
           F      +DA +   VEG     ++N G+ CT   R+  Q+ IY+  +  +    A +K 
Sbjct: 272 FADVLDQEDAFVSKAVEGA-VLAFFNQGEVCTCPSRLLIQESIYEKFIGMVVERSAQIKR 330

Query: 310 GAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGN-----GYYYAPTL 364
           G P D    +G  +S    +++   ++  K  G  +VITGG     +     GYY  PTL
Sbjct: 331 GNPLDTEVMVGAQASQEQYDKILSYIQIGKDEG-AEVITGGAVETMSADYCEGYYIQPTL 389

Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424
           L G   +  + Q+E+FGPVVSVT F +E + +  AND ++GL + VWT+D+ RA+R+   
Sbjct: 390 LKGT-NNMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWTRDMNRAYRMGRG 448

Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           +Q G  W N + M  +    GG K SG G++     L+ Y   ++++V +
Sbjct: 449 IQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLVSY 498


Lambda     K      H
   0.317    0.134    0.397 

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: 571
Number of extensions: 23
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
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