GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Magnetospirillum magneticum AMB-1

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_011382625.1 AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= SwissProt::Q0AVM1
         (260 letters)



>NCBI__GCF_000009985.1:WP_011382625.1
          Length = 261

 Score =  134 bits (338), Expect = 1e-36
 Identities = 85/258 (32%), Positives = 133/258 (51%), Gaps = 6/258 (2%)

Query: 4   ENIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFV 63
           E I++ +   +  + +NRP  +NA N +    ++ AV    +D     L+ITG+G K F 
Sbjct: 3   ETILVARTGDVTTITLNRPGRINAFNVEMHGALRSAVAHAAED-GTRCLVITGAG-KGFC 60

Query: 64  AGADIAFMQNLSAMEAREFGAL----GQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCC 119
           AG D++   +       + GA        + R ++A+  PVIAAVNG A G G  LA+ C
Sbjct: 61  AGQDLSDRVSKPGDPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALAC 120

Query: 120 DFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLV 179
           D  +AA +A F Q    +G+ P  GGT  LPRLVG   A  L+   + + A++A + G++
Sbjct: 121 DIVVAARSAAFVQSFCKVGLIPDSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGMI 180

Query: 180 NKVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFAT 239
            + V  E+LLP V  +A ++ ++    + L K A        +D  + +E D       T
Sbjct: 181 WRCVDDEQLLPTVLAMAAQLAAQPTRGLALMKKALARSGANTLDAQLDLERDLQTEAGCT 240

Query: 240 QDQKEGMTAFLEKRKANF 257
           QD +EG+ AF+EKR   F
Sbjct: 241 QDYQEGVRAFMEKRPPRF 258


Lambda     K      H
   0.319    0.136    0.378 

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: 157
Number of extensions: 9
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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: 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 (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