GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Desulfacinum infernum DSM 9756

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate WP_073038547.1 BUB04_RS08370 CaiB/BaiF CoA-transferase family protein

Query= SwissProt::Q9HAC7
         (445 letters)



>NCBI__GCF_900129305.1:WP_073038547.1
          Length = 392

 Score =  229 bits (583), Expect = 2e-64
 Identities = 140/396 (35%), Positives = 218/396 (55%), Gaps = 10/396 (2%)

Query: 47  PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106
           P EG+++LDL+R+L GPF +M L DLGA+VIKVE P  GD  R W PP +G  S +++ +
Sbjct: 4   PFEGIRVLDLSRLLPGPFCSMLLADLGADVIKVEDPKVGDYIRWW-PPKIGANSGFHVVL 62

Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166
           NRNK+S+ +N+K+P G  +   LAA  DV +E + PG +  +G+GY  + E+ P IIYC+
Sbjct: 63  NRNKRSLTLNLKEPAGRDVFVRLAASADVVLEGFRPGVMDRLGVGYGALREVNPRIIYCA 122

Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATG-LYAYGAIMA 225
           ITGYGQ GP + RAG+D    A+SG++   G   GDPV PGV + DL  G L A  +I A
Sbjct: 123 ITGYGQDGPRADRAGHDINYLALSGVLSYCG-RGGDPVVPGVQIGDLGGGALTAAFSIAA 181

Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLI-GQKEAKRWGTAHGSIVPYQAFKTK 284
            L  + +TG+G  ID ++     A        +L  G+         +  +  Y  ++T+
Sbjct: 182 ALFWRERTGEGQMIDISMTDGAAAWNCLRWGKFLADGRVPEPGDDLLNHGLACYDVYRTR 241

Query: 285 DG-YIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTS 343
           DG ++ +GA   Q +   C+++  P+      ++       ++KEL   ++E F  +  +
Sbjct: 242 DGRHMSLGALEPQFWKAFCRVMGRPDWDRPDYFQPG----PHQKELRDQVAEAFAGKTQA 297

Query: 344 KWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMS 403
           +W+ +FE       P+ N+  V  +  + H  +V+E+ H   G     G A ++SK    
Sbjct: 298 QWVRIFEAEDCCCEPVLNLAEVLDDEAMRHRRMVVELHHQAWGAYRQMGLAPKFSKTSGE 357

Query: 404 EARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439
                P LG+HT  +L E   YD+ AI +L + GVV
Sbjct: 358 IRTHAPDLGEHTRDVLLEA-GYDEGAIEKLRAEGVV 392


Lambda     K      H
   0.318    0.137    0.410 

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: 474
Number of extensions: 21
Number of successful extensions: 4
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: 445
Length of database: 392
Length adjustment: 32
Effective length of query: 413
Effective length of database: 360
Effective search space:   148680
Effective search space used:   148680
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: 50 (23.9 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