GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Rhizobium etli CFN 42

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-15732
         (497 letters)



>NCBI__GCF_000092045.1:WP_011425015.1
          Length = 506

 Score =  353 bits (906), Expect = e-102
 Identities = 196/480 (40%), Positives = 278/480 (57%), Gaps = 11/480 (2%)

Query: 17  RKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSR 76
           R  KM I   W+  AS   +    P+ G  +   PA  A D +RA+ AAR+AFD+ PW R
Sbjct: 16  RDFKMLIDGKWEAGAS-HPIERIAPSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPR 74

Query: 77  LRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVM-DVQLAIDFLRYMAGWAT 135
           +   ER  +L + ADL+   A +LA L+ +  GK   + QV  ++  ++D  RY A  A 
Sbjct: 75  MTASERSAILLKAADLIAARAEELAFLDAIEAGKP--ITQVRGEIAGSVDIWRYAAALAR 132

Query: 136 KIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVL 195
            + G +          D   G V REAIGVV  I  WNFP L+   KL  ALA GCT V+
Sbjct: 133 DLHGESYNTL-----GDGTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVV 187

Query: 196 KPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGK 255
           KP++ T  S L L E++ +AG P GV N+VTGTG   GA ++ HP VD ++FTGST VGK
Sbjct: 188 KPSELTSGSTLVLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGK 247

Query: 256 LIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHR 315
           L  K A   + +V+LELGGK+P IV PDA+L      A    +FN G+ C AGSRL +H+
Sbjct: 248 LTMKNAAQTLKKVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHK 307

Query: 316 KHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGE 375
               +VV  +A ++ G+K+G+ LDP  Q+G +I+ +  ++++GY+   R  GA V  GGE
Sbjct: 308 SIASDVVRRVAELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGE 367

Query: 376 --GFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASI 433
               G G F+ PT++  V     + +EE+FGPVL  + F+   E + +AN   YGL A +
Sbjct: 368 TLDLGMGQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGV 427

Query: 434 WSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSV 493
           WS D      +   +++G++W+N        LPFGGYK SG+GRE+G  A+E YTE K++
Sbjct: 428 WSRDFDTCLTIGRSVRAGTIWMNTFMDGASELPFGGYKQSGLGRELGRHAVEDYTETKTL 487


Lambda     K      H
   0.320    0.137    0.413 

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: 588
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: 497
Length of database: 506
Length adjustment: 34
Effective length of query: 463
Effective length of database: 472
Effective search space:   218536
Effective search space used:   218536
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