GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaF in Magnetospirillum magneticum AMB-1

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011382625.1 AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= BRENDA::P76082
         (255 letters)



>lcl|NCBI__GCF_000009985.1:WP_011382625.1 AMB_RS00905
           2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
          Length = 261

 Score =  152 bits (384), Expect = 7e-42
 Identities = 102/262 (38%), Positives = 145/262 (55%), Gaps = 8/262 (3%)

Query: 1   MSE-LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFF 59
           MSE ++V+R   V  +TLNRP   NA N  +   L + +  AA D +  + VITG  + F
Sbjct: 1   MSETILVARTGDVTTITLNRPGRINAFNVEMHGALRSAVAHAAEDGTRCL-VITGAGKGF 59

Query: 60  AAGADLNEMAEK------DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALL 113
            AG DL++   K      DL A+L+     L   L+A   P+IAAVNG A GAG  LAL 
Sbjct: 60  CAGQDLSDRVSKPGDPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALA 119

Query: 114 CDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGL 173
           CD+VVA  +A F      +G++P +GGT  L R VG + A+ +++ GE +TA+QA Q G+
Sbjct: 120 CDIVVAARSAAFVQSFCKVGLIPDSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGM 179

Query: 174 VSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAA 233
           +      +  L   L +A+++A      L   K+AL +S    L A L  ER L T    
Sbjct: 180 IWRCVDDEQLLPTVLAMAAQLAAQPTRGLALMKKALARSGANTLDAQLDLERDLQTEAGC 239

Query: 234 TEDRHEGISAFLQKRTPDFKGR 255
           T+D  EG+ AF++KR P F+GR
Sbjct: 240 TQDYQEGVRAFMEKRPPRFEGR 261


Lambda     K      H
   0.318    0.130    0.356 

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: 124
Number of extensions: 6
Number of successful extensions: 2
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: 255
Length of database: 261
Length adjustment: 24
Effective length of query: 231
Effective length of database: 237
Effective search space:    54747
Effective search space used:    54747
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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