Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate 6939203 Sama_3297 hypothetical protein (RefSeq)
Query= BRENDA::Q8EJW4 (397 letters) >FitnessBrowser__SB2B:6939203 Length = 396 Score = 602 bits (1551), Expect = e-177 Identities = 300/396 (75%), Positives = 340/396 (85%), Gaps = 5/396 (1%) Query: 5 LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGM 64 +F PQI++ ATYMRGGTSKGVFFRL DLPEAA+VPG RDALLLRVIGSPDPY K DGM Sbjct: 1 MFKPQIRIPATYMRGGTSKGVFFRLDDLPEAARVPGAERDALLLRVIGSPDPYGKHTDGM 60 Query: 65 GGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLI 124 GGATSSTSK VI++ SS HDVDYL+GQVSID FVDWSGNCGNL+ A GAFAI GL+ Sbjct: 61 GGATSSTSKCVIMNKSSVPGHDVDYLYGQVSIDTAFVDWSGNCGNLSTAAGAFAIHAGLV 120 Query: 125 DAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNP 184 DA+R+P NG+C VRIWQANIGKTIIAHVP+T+G VQETGDFELDGVTFPAAE+ +EF++P Sbjct: 121 DASRVPENGICEVRIWQANIGKTIIAHVPVTNGEVQETGDFELDGVTFPAAEIVLEFVDP 180 Query: 185 AADDDGEGGCMFPTGNLVDVLEVPG----IGRFNATMINAGIPTIFINAEDLGYTGTELQ 240 ADD +GG MFPTGNLVD LEVP G+ AT+INAGIPTIF+NAEDLGY G ELQ Sbjct: 181 -ADDGEDGGAMFPTGNLVDELEVPSEVHPSGKIRATLINAGIPTIFVNAEDLGYRGDELQ 239 Query: 241 DDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVA 300 + IN + ALA FE +RAHGA+RMGLIK +DEA +RQHTPK+AFV P ++ SSGKTVA Sbjct: 240 EAINGNPVALAMFEQLRAHGAIRMGLIKTLDEAKTRQHTPKVAFVTNPMTHVVSSGKTVA 299 Query: 301 AEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTL 360 ++VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGE++AVRFGHPSGTL Sbjct: 300 EDEVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERQAVRFGHPSGTL 359 Query: 361 RVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPK 396 RVGA+A Q +G+WTV KAIMSRSAR+LMEG VRVP+ Sbjct: 360 RVGAEAKQVDGQWTVTKAIMSRSARILMEGTVRVPQ 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: 612 Number of extensions: 20 Number of successful extensions: 3 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 Apr 09 2024. 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