GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Acidithiobacillus ferrooxidans ATCC 23270

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_000021485.1:WP_012536996.1
          Length = 506

 Score =  160 bits (404), Expect = 1e-43
 Identities = 145/477 (30%), Positives = 224/477 (46%), Gaps = 30/477 (6%)

Query: 5   FIDGAWVDGA-GPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63
           FI G WV    G  F + +P   +   +   +SA+D+E A+ +A  A  AW    + AR 
Sbjct: 22  FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAAKDAWGRTSVTARS 81

Query: 64  TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123
            I+ + A  +    E LA     + GK + E      ++ A V +S   +    G  RA 
Sbjct: 82  NILLKIADRIDANLEMLAVAETWDNGKAVRE------TLNADVPLSSDHFRYFAGCLRAQ 135

Query: 124 MA-------DGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPG 176
                    + VA   H P GVV    P+NFP  +    + PAL AGN VV KP+E  P 
Sbjct: 136 EGTIGEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPA 195

Query: 177 VARATVEIWRDAGLPAGVLNLVQGEK-DTGVALANHRQIDGLFFTGSSDTGTLLHKQFGG 235
                +E+  D  LPAGVLN+V G   + G ALA  ++I  + FTGS+  G+L+ K +  
Sbjct: 196 SILVMMELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMK-YAA 253

Query: 236 RPEIVLALEMGGNNP-LVVAEVEDI-DAAVHHAIQSA---FLSAGQRCTCARRILVPRGA 290
              I   +E+GG +P +  A+V D  DA V  A++ A   F + G+ CTC  R+L+    
Sbjct: 254 ENIIPSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLAFFNQGEVCTCPSRLLIQESI 313

Query: 291 FGDRFVARLADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPI---- 346
           + ++F+  + + +++I       D +  +GA  S     ++++        GA  I    
Sbjct: 314 Y-EKFIGMVVERSAQIKRGN-PLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGA 371

Query: 347 IEMKQRDPALGF-VNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLS 405
           +E    D   G+ +   +L  TN   +  EE FGP+  +  + D  +A+A AND  FGL 
Sbjct: 372 VETMSADYCEGYYIQPTLLKGTNNMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLG 431

Query: 406 AGLLADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAADY 462
           AG+   D    +   R I+AG V W    +   + A FGG  +SG  R +     D+
Sbjct: 432 AGVWTRDMNRAYRMGRGIQAGRV-WTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDH 487


Lambda     K      H
   0.320    0.134    0.402 

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: 476
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: 487
Length of database: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
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