Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_045580431.1 AL072_RS10180 2-methylaconitate cis-trans isomerase PrpF
Query= SwissProt::Q937N7 (396 letters) >NCBI__GCF_001305595.1:WP_045580431.1 Length = 405 Score = 576 bits (1485), Expect = e-169 Identities = 291/405 (71%), Positives = 323/405 (79%), Gaps = 9/405 (2%) Query: 1 MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60 M PQI+IPATY+RGGTSKG+FFRL DLPE +V G ARD L +RVIGSPDPY + IDG Sbjct: 1 MASAPQIRIPATYMRGGTSKGIFFRLDDLPERCRVAGAARDRLFLRVIGSPDPYARHIDG 60 Query: 61 MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 MG ATSSTSK VILSKS RP HDVDYL+GQVSID FVDWSGNCGNLS A G FAI AGL Sbjct: 61 MGGATSSTSKAVILSKSARPGHDVDYLYGQVSIDSAFVDWSGNCGNLSTAAGAFAIHAGL 120 Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180 +D +R+P NGV VRIWQANIGKTI+ HVP T G VQETGDFELDGVTFPAAE+ LEF+D Sbjct: 121 MDPARVPENGVCTVRIWQANIGKTIVAHVPATGGLVQETGDFELDGVTFPAAEIVLEFLD 180 Query: 181 PAAEEE-----GAGGAMFPTGNVVDDLEVP----AVGTLKATMINAGIPTIFVNAESIGY 231 PA E + G G+MFPTGN++D LEVP G LKAT+I+AGIPTIFV A +GY Sbjct: 181 PAEEGDSGGAGGGNGSMFPTGNLIDTLEVPDSLVPGGRLKATLIDAGIPTIFVAAADLGY 240 Query: 232 TGTELQDAINSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVAS 291 GTELQ+AIN D ALA FE GALRMGLIK EAA+RQHTPK+AFV D+V S Sbjct: 241 RGTELQEAINGDAAALARFEALRTIGALRMGLIKEPGEAARRQHTPKIAFVAPPADHVVS 300 Query: 292 SGKKVAAADVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFG 351 SG+ V A +VDLLVRALSMGKLHHAMMGTA+VAI AAA+PGTLVNLAAGGG R AVRFG Sbjct: 301 SGRTVGAGEVDLLVRALSMGKLHHAMMGTASVAIAAAAAVPGTLVNLAAGGGARTAVRFG 360 Query: 352 HPSGTLRVGAEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396 HPSG+LRVGAEA VDG W V KA+MSRSAR+LMEGWVRVP D+F Sbjct: 361 HPSGSLRVGAEAVPVDGRWTVTKAVMSRSARILMEGWVRVPADSF 405 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: 568 Number of extensions: 17 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: 396 Length of database: 405 Length adjustment: 31 Effective length of query: 365 Effective length of database: 374 Effective search space: 136510 Effective search space used: 136510 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