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.
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:
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