Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_020306354.1 PST_RS10320 2-methylaconitate cis-trans isomerase PrpF
Query= SwissProt::Q937N7 (396 letters) >NCBI__GCF_000013785.1:WP_020306354.1 Length = 395 Score = 624 bits (1610), Expect = 0.0 Identities = 310/396 (78%), Positives = 341/396 (86%), Gaps = 1/396 (0%) Query: 1 MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60 M H+PQI+IPATY+RGGTSKGVFFRLQDLP++ QVPG ARD L MRVIGSPDPY IDG Sbjct: 1 MAHLPQIRIPATYMRGGTSKGVFFRLQDLPQSCQVPGAARDKLFMRVIGSPDPYSAHIDG 60 Query: 61 MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 MG ATSSTSK VILSKS+RPDHDV+YL+GQVSID+PFVDWSGNCGNLS G FA+ AGL Sbjct: 61 MGGATSSTSKCVILSKSSRPDHDVEYLYGQVSIDKPFVDWSGNCGNLSTGAGAFALHAGL 120 Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180 VDASRIP NG VVRIWQANIGKTII HVPV NG+VQETGDFELDGVTFPAAE+ LEF+D Sbjct: 121 VDASRIPDNGTCVVRIWQANIGKTIIAHVPVANGQVQETGDFELDGVTFPAAEIVLEFLD 180 Query: 181 PAAEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAI 240 P+ + E GG+MFPTGN+VDDLEVP +GTLKATMI+AGIPT+FVNAE IGY GTEL++ I Sbjct: 181 PSDDGE-EGGSMFPTGNLVDDLEVPGIGTLKATMISAGIPTVFVNAEDIGYQGTELREDI 239 Query: 241 NSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAAD 300 N + ALA E GALRMGLIK +EA RQHTPKVAFV + Y ASSGK + A + Sbjct: 240 NGNPEALARLESIRVAGALRMGLIKTAEEALTRQHTPKVAFVSRPKSYRASSGKNIEAGE 299 Query: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVG 360 VDLLVRALSMGKLHHAMMGT AVAIGTAAA+PGTLVNLAAGGGER AVRFGHPSGTLRVG Sbjct: 300 VDLLVRALSMGKLHHAMMGTCAVAIGTAAAVPGTLVNLAAGGGERQAVRFGHPSGTLRVG 359 Query: 361 AEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396 AEA+Q+DG+W V KAIMSRSARVLMEGWVRVPGDAF Sbjct: 360 AEAKQIDGQWTVTKAIMSRSARVLMEGWVRVPGDAF 395 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: 575 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: 396 Length of database: 395 Length adjustment: 31 Effective length of query: 365 Effective length of database: 364 Effective search space: 132860 Effective search space used: 132860 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