Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate Ac3H11_2325 2-methylaconitate cis-trans isomerase
Query= BRENDA::Q8EJW4 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2325 Length = 396 Score = 609 bits (1570), Expect = e-179 Identities = 304/389 (78%), Positives = 340/389 (87%), Gaps = 1/389 (0%) Query: 7 PPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGG 66 P QIKV ATY+RGGTSKGVFF L+DLP AQ PGPARDALLLRV+GSPDPY KQIDGMG Sbjct: 5 PHQIKVPATYLRGGTSKGVFFLLEDLPAPAQQPGPARDALLLRVLGSPDPYGKQIDGMGN 64 Query: 67 ATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDA 126 A+SSTSK VILS S++ HDVDYLFGQVSI++PFVDWSGNCGNL+AAVG AI GLIDA Sbjct: 65 ASSSTSKAVILSRSTRPGHDVDYLFGQVSINQPFVDWSGNCGNLSAAVGPCAIHMGLIDA 124 Query: 127 ARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAA 186 ARIP+NG VRIWQANIGKTI+AHVPIT G VQETGDFELDGVTF AAEV +EFM+PA Sbjct: 125 ARIPQNGTIPVRIWQANIGKTIVAHVPITHGQVQETGDFELDGVTFAAAEVALEFMDPA- 183 Query: 187 DDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSD 246 DD EGG MFPTGN+VD LEVPG+G F AT+INAGIPTIF+NA++LGYTGTELQ IN D Sbjct: 184 DDGDEGGGMFPTGNVVDTLEVPGVGSFAATLINAGIPTIFLNAQELGYTGTELQGAINGD 243 Query: 247 NAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDL 306 ALA+FE IRAHGALRMGLI+H+ EA +RQHTPKIAFVAP SY +SSGK + A+D+DL Sbjct: 244 AVALARFEAIRAHGALRMGLIQHLGEATTRQHTPKIAFVAPRASYTASSGKAIDAKDIDL 303 Query: 307 LVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQA 366 LVRA+SMG+LHHAMMGTAAVAIGTAAAIPGTLVNLAAGGG + +VRFGHPSGTLRVGA+A Sbjct: 304 LVRAISMGQLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGVRSSVRFGHPSGTLRVGAEA 363 Query: 367 VQENGEWTVIKAIMSRSARVLMEGFVRVP 395 Q NG+W V KA+MSRSAR+LMEG+VRVP Sbjct: 364 AQINGQWKVTKALMSRSARILMEGWVRVP 392 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: 596 Number of extensions: 18 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: 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 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