GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Acidithiobacillus ferrooxidans ATCC 23270

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  367 bits (941), Expect = e-106
 Identities = 209/488 (42%), Positives = 290/488 (59%), Gaps = 20/488 (4%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           FI  +W   V  + F  + P  G+   Q A    ED++ A+ AA A   +   W +   +
Sbjct: 22  FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHA---IADKWGKTSPA 78

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R  +L ++AD IE +   LA  ET+DNGKP   +   D+ + +   RY+AG      G 
Sbjct: 79  ERANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEGG 138

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
              ID +  +Y  HEP+GV GQIIPWNFP+LM +WKL PAL  GNVVV+K AE TP++ L
Sbjct: 139 ISDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISIL 198

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +A LI +   PPGV+NIV G+G  AG  +A+ + + K+AFTGST  GRVI  AA +S L
Sbjct: 199 ILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANS-L 256

Query: 280 KRVTLELGGKSPNIIMS------DADMDWAVEQAHFALF-FNQGQCCCAGSRTFVQEDIY 332
              TLELGGKSPNI  +      D+ +D A+E     LF FNQG+ C   SR  +QE IY
Sbjct: 257 IPATLELGGKSPNIFFADVMDKDDSFLDKAIE--GLVLFAFNQGEVCTCPSRALIQESIY 314

Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA- 391
           D+F+ER + R K+   GNP D+ T  G Q  + Q  KIL Y++ GKQEGA++L GG  A 
Sbjct: 315 DKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAI 374

Query: 392 ----ADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447
                D GY++QPT+F    + M I +EEIFGPV+ +  FK   E +  AN++ YGL A 
Sbjct: 375 VDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAG 433

Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507
           V++++ + A  + +A++AG VW+NCY  + A + FGGYK SG GRE  +  L  Y + K 
Sbjct: 434 VWSRNGNVAYRMGRAIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTKN 493

Query: 508 VTVKVPQK 515
           + V   ++
Sbjct: 494 LLVSYAEQ 501


Lambda     K      H
   0.319    0.136    0.409 

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: 623
Number of extensions: 34
Number of successful extensions: 6
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: 517
Length of database: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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