GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Rhizobium etli CFN 42

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein

Query= BRENDA::Q97YT9
         (492 letters)



>NCBI__GCF_000092045.1:WP_011425015.1
          Length = 506

 Score =  221 bits (562), Expect = 6e-62
 Identities = 146/476 (30%), Positives = 248/476 (52%), Gaps = 10/476 (2%)

Query: 16  KLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEK--WREVPI 73
           K+ I+G++    +  I +   P+    ++  P  +  + E AI +A++AF++  W  +  
Sbjct: 19  KMLIDGKWEAGASHPIERIA-PSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMTA 77

Query: 74  TTRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKG 133
           + R   L    + +   +E +A +     GK I + RG++  +++    A + A  L+ G
Sbjct: 78  SERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYAAALARDLH-G 136

Query: 134 EHLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVP 193
           E  + +       V+RE +GV  IITP+NFP ++    LP+A+  G T VVKPSE+T   
Sbjct: 137 ESYNTLGDGTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTSGS 196

Query: 194 MDFIIRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKL-VQGVTFVGSTRVGKYIYENAGKN 252
              +  I  +  +P GVVN+V G    V   +T+   V  ++F GST VGK   +NA + 
Sbjct: 197 TLVLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKNAAQT 256

Query: 253 GKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRK 312
            KK  ++ G KN  +V PDADL+  I + V   + NAG+ C A + L+   +I  +V R+
Sbjct: 257 LKKVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASDVVRR 316

Query: 313 FIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPN 372
             E SK +K+G  LD    +G ++T    ++I GY+      GA++   G  +   +   
Sbjct: 317 VAELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETL---DLGM 373

Query: 373 GYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGY 432
           G F+ PT+ + VTP+M +A+EE+FGPV S++  +   EA+ I N  +YG ++ +++    
Sbjct: 374 GQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDFD 433

Query: 433 YARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFTDKKVV 488
                 R V  G I +N  +    +  PFGG K+S  G   G+  +V+ +T+ K +
Sbjct: 434 TCLTIGRSVRAGTIWMNTFMDG-ASELPFGGYKQSGLGRELGR-HAVEDYTETKTL 487


Lambda     K      H
   0.319    0.139    0.398 

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: 550
Number of extensions: 21
Number of successful extensions: 3
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: 492
Length of database: 506
Length adjustment: 34
Effective length of query: 458
Effective length of database: 472
Effective search space:   216176
Effective search space used:   216176
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 (21.7 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