GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Shewanella loihica PV-4

Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate 5209349 Shew_1823 putative AcnD-accessory protein PrpF (RefSeq)

Query= BRENDA::Q8EJW4
         (397 letters)



>FitnessBrowser__PV4:5209349
          Length = 389

 Score =  586 bits (1510), Expect = e-172
 Identities = 297/388 (76%), Positives = 334/388 (86%), Gaps = 4/388 (1%)

Query: 9   QIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGAT 68
           Q+K+ ATYMRGGTSKGVFF L+DLP  AQ PGPARDALLLRVIGSPDPY KQ DGMGGAT
Sbjct: 3   QMKIPATYMRGGTSKGVFFALKDLPLNAQQPGPARDALLLRVIGSPDPYGKQTDGMGGAT 62

Query: 69  SSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAAR 128
           SSTSKTVIL  S + +HDVDYLFGQV+IDKPFVDWSGNCGNLTAAVGAFAI+ GL+D+A+
Sbjct: 63  SSTSKTVILDKSQRDDHDVDYLFGQVAIDKPFVDWSGNCGNLTAAVGAFAITQGLVDSAK 122

Query: 129 IPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADD 188
           IP NG+  V+IWQANI KTIIAHVP+ DG VQE GDFELDGVTFPAAEV +EF++PA   
Sbjct: 123 IPDNGIAVVKIWQANINKTIIAHVPMVDGEVQELGDFELDGVTFPAAEVLVEFVDPA--- 179

Query: 189 DGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNA 248
           DGEG  MFPTGNLVD LEVPG   F+AT INAGIPTIF+ AE LGY GTELQ+ IN D A
Sbjct: 180 DGEGD-MFPTGNLVDKLEVPGEPVFDATFINAGIPTIFLKAEQLGYEGTELQEAINGDAA 238

Query: 249 ALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLV 308
           AL +FETIRAHGAL+MGLI+ +DEAA RQHTPKIAFVAP K+Y SSSGK +AAE++DL V
Sbjct: 239 ALERFETIRAHGALQMGLIQSLDEAAGRQHTPKIAFVAPAKAYTSSSGKQIAAEEIDLHV 298

Query: 309 RALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQ 368
           RALSMGKLHHAMMGTAAVAIGTAA+IPGTLVN AAGG  +E+VRFGHPSGTL+VGA+A +
Sbjct: 299 RALSMGKLHHAMMGTAAVAIGTAASIPGTLVNQAAGGQARESVRFGHPSGTLKVGAKASE 358

Query: 369 ENGEWTVIKAIMSRSARVLMEGFVRVPK 396
           + G W V K  MSRSARVLM+G+V VP+
Sbjct: 359 QEGRWQVEKVSMSRSARVLMQGWVCVPE 386


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: 520
Number of extensions: 16
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: 397
Length of database: 389
Length adjustment: 31
Effective length of query: 366
Effective length of database: 358
Effective search space:   131028
Effective search space used:   131028
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