GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Shewanella sp. ANA-3

Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate 7026695 Shewana3_3828 methylitaconate delta2-delta3-isomerase (RefSeq)

Query= BRENDA::Q8EJW4
         (397 letters)



>FitnessBrowser__ANA3:7026695
          Length = 397

 Score =  729 bits (1881), Expect = 0.0
 Identities = 366/395 (92%), Positives = 378/395 (95%)

Query: 1   MSNKLFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQ 60
           MS   FPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPY KQ
Sbjct: 1   MSKNPFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYGKQ 60

Query: 61  IDGMGGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAIS 120
           IDGMGGATSSTSKTVILS S++A+HDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAIS
Sbjct: 61  IDGMGGATSSTSKTVILSKSTQADHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAIS 120

Query: 121 NGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIE 180
           NGLIDA RIP+NG+CTVRIWQANI KTIIAHVPIT+G VQETGDFELDGVTFPAAEVQIE
Sbjct: 121 NGLIDAERIPQNGICTVRIWQANIAKTIIAHVPITNGEVQETGDFELDGVTFPAAEVQIE 180

Query: 181 FMNPAADDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQ 240
           FMNPAAD+DG+ G MFPTGNLVDVLEVPGIG FNATMINAGIPTIFINAEDLGYTGTELQ
Sbjct: 181 FMNPAADEDGDSGSMFPTGNLVDVLEVPGIGSFNATMINAGIPTIFINAEDLGYTGTELQ 240

Query: 241 DDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVA 300
           DDINSDNAALAKFETIRAHGA+RMGLIKHIDEAASRQHTPK+AFVA P SY SSSGK VA
Sbjct: 241 DDINSDNAALAKFETIRAHGAVRMGLIKHIDEAASRQHTPKVAFVAKPTSYVSSSGKAVA 300

Query: 301 AEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTL 360
           AE++DLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTL
Sbjct: 301 AEEIDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTL 360

Query: 361 RVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVP 395
           RVGAQA  ENGEWTVIKAIMSRSARVLMEGFVRVP
Sbjct: 361 RVGAQATLENGEWTVIKAIMSRSARVLMEGFVRVP 395


Lambda     K      H
   0.318    0.134    0.393 

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: 650
Number of extensions: 12
Number of successful extensions: 1
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 (21.7 bits)
S2: 50 (23.9 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