GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sulfurimonas denitrificans DSM 1251

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::Q97XA5
         (470 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  255 bits (652), Expect = 2e-72
 Identities = 157/458 (34%), Positives = 253/458 (55%), Gaps = 10/458 (2%)

Query: 11  SPSNLKVIGTVKRMSKDEVRGEIEEAYKGFEIISRMPLYKRTAILRKISEILEREQERLA 70
           +P N +V       + D+ +  +  A    +  S+  + +R + L  ++  L + +E +A
Sbjct: 22  NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81

Query: 71  RLLAMEAGKPISDSRVEVLRASRLFRQAAEEVGIVLEGKNYRVDAYEYPPGNENRIVLST 130
           + +  E GKPI+ SR+EV R       AAE +   + G+    DA+      +  I   +
Sbjct: 82  KTITDEVGKPITYSRIEVERCIETVTLAAETMR-TMHGETVNTDAFA---SGKKTISFFS 137

Query: 131 REPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKILVEAGLP- 189
           R P GVV AI PFNFP+N  AHK+APAL  GN+V++KP+   PL A +  K+ +E+    
Sbjct: 138 RVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAI 197

Query: 190 DSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKRIIMELGGSDPI 249
             A+ VV G  +++G  ++T  +  +I+ TGS   G +I +K+  + K++ +ELGG+   
Sbjct: 198 KDALSVVYG-DADVGGTLVTSEIPRVISFTGSVGVG-EIITKSAGI-KKVSLELGGNAAT 254

Query: 250 IILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFNEKAKALKVGEPL 309
            I + AN++ A+       F  +GQ C + +RI V +++Y +F     E  K L VG P 
Sbjct: 255 FIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPY 314

Query: 310 DETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPESGSFFPLTMVTNPSLDMLVL 369
           +E T +GP++N E+ +     ++ A +K G   IL    E   F+P  M  +   DM ++
Sbjct: 315 EEDTFMGPLVNDEAAKRAMEWVQSA-IKEGATPILEPRVEGRVFYPCVMA-DVKEDMAIV 372

Query: 370 KSEVFGPIVPIVSVKSDEEAIRIANSTEYGLQSAIFTNDVNRALKLSRELKFGAVIINDS 429
             EVF PIV ++ VK  +EA+ + N++ YGLQ +IFTND+N   +   EL  G ++IND 
Sbjct: 373 CQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDM 432

Query: 430 TRLRWDSLPFGGFKKTGIGREGVRETMLEMTENKLIAI 467
             LR+D  P+GG K +G+GREG R  + EM+E K + I
Sbjct: 433 PTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.316    0.135    0.366 

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: 507
Number of extensions: 28
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: 470
Length of database: 471
Length adjustment: 33
Effective length of query: 437
Effective length of database: 438
Effective search space:   191406
Effective search space used:   191406
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: 51 (24.3 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