Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_035701937.1 BA79_RS07240 3-methylitaconate isomerase
Query= SwissProt::Q937N7 (396 letters) >NCBI__GCF_000691145.1:WP_035701937.1 Length = 376 Score = 208 bits (530), Expect = 2e-58 Identities = 139/388 (35%), Positives = 202/388 (52%), Gaps = 36/388 (9%) Query: 8 KIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDGMGAATSS 67 K+P T +RGGTSKGVF + D P + L+ ++GSPD Q+DG+G S Sbjct: 3 KVPITIMRGGTSKGVFIQANDAPYEHD----ELEEFLLDIMGSPDRL--QVDGIGGGNSL 56 Query: 68 TSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGLVDASRIP 127 TSK I+ K+TRPD DV+Y F QVSI++ FVD+ GNCGN+S+AVGP+AI GLV A Sbjct: 57 TSKVAIIDKATRPDVDVNYTFAQVSINERFVDFKGNCGNISSAVGPYAIIKGLVQAV--- 113 Query: 128 HNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMDPAAEEEG 187 V VRI N K I+ V V NGEV+ G E+ GV + + L F P E Sbjct: 114 -EPVTTVRILNTNTNKIIVAEVEVENGEVKFEGQAEIPGVKGTGSPIYLSFEKP---EGA 169 Query: 188 AGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTEL----QDAINSD 243 G FPTGN +D ++ G + ++++ P FV A+ I GTEL D + D Sbjct: 170 VTGKTFPTGNKMDTIQT-KFGEIPISIVDIANPIAFVRAKDIQLKGTELPEEFTDELLDD 228 Query: 244 TRALAMFEDHPCYGALRMGLIKNVDEAAKRQH--TPKVAFVRQAGDYVASSGKKVAAADV 301 + C+ A + E A Q PK+A + + DYV ++G AAD+ Sbjct: 229 LEEIRSIAAEMCHFAPK--------ELATLQSPAVPKLAIISEPADYVDTNGILRRAADM 280 Query: 302 DLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVGA 361 D++VR LSM + H A+ T +V + + + TL G+ + +R GHP+G ++ Sbjct: 281 DIIVRMLSMQRPHQALAITGSVCVSASCFMDQTL-PAQLFEGQDDTLRIGHPAGIMQTEI 339 Query: 362 EAQQVDGEWAVKKAIMSRSARVLMEGWV 389 + Q + + R+AR +++G V Sbjct: 340 DISQ-------NRVKVIRTAREILDGVV 360 Lambda K H 0.317 0.134 0.394 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: 338 Number of extensions: 18 Number of successful extensions: 6 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: 396 Length of database: 376 Length adjustment: 30 Effective length of query: 366 Effective length of database: 346 Effective search space: 126636 Effective search space used: 126636 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 24 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