Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_013091179.1 BC1002_RS16730 2-methylaconitate cis-trans isomerase PrpF
Query= SwissProt::Q937N7 (396 letters) >NCBI__GCF_000092885.1:WP_013091179.1 Length = 394 Score = 662 bits (1707), Expect = 0.0 Identities = 332/390 (85%), Positives = 357/390 (91%) Query: 3 HVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDGMG 62 H PQI+IPATY+RGGTSKGVFFRLQDLP+ AQ PG ARDALLMRVIGSPDPYGKQIDGMG Sbjct: 2 HSPQIRIPATYMRGGTSKGVFFRLQDLPDDAQRPGAARDALLMRVIGSPDPYGKQIDGMG 61 Query: 63 AATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGLVD 122 ATSSTSKTVI+S+S+RPDHDVDYLFGQVSID+ FVDWSGNCGNLSAAVGPFAISAGLVD Sbjct: 62 GATSSTSKTVIISRSSRPDHDVDYLFGQVSIDKAFVDWSGNCGNLSAAVGPFAISAGLVD 121 Query: 123 ASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMDPA 182 ASR+P +GVA+VRIWQANIGKTII HVP+T+G VQETGDFELDGVTFPAAEV LEFM+PA Sbjct: 122 ASRVPRDGVAIVRIWQANIGKTIIAHVPMTDGAVQETGDFELDGVTFPAAEVPLEFMNPA 181 Query: 183 AEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAINS 242 A+EEGAGGAMFPTGN+VDDLEVP VGTLKATMINAGIPTIFV+AE+IGY GTELQDAINS Sbjct: 182 ADEEGAGGAMFPTGNLVDDLEVPGVGTLKATMINAGIPTIFVDAEAIGYKGTELQDAINS 241 Query: 243 DTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAADVD 302 D +ALAMFE +GALRMGLIKN+DE A RQHTPKVAFV + DYVASSGK V A DVD Sbjct: 242 DAKALAMFETIRAHGALRMGLIKNLDEIATRQHTPKVAFVAKPVDYVASSGKPVRAGDVD 301 Query: 303 LLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVGAE 362 LLVRA+SMGKLHHAMMGTAAVAIGTAAAI GTLVN AAGGGER +VRFGHPSGTLRVGA+ Sbjct: 302 LLVRAMSMGKLHHAMMGTAAVAIGTAAAIAGTLVNQAAGGGERESVRFGHPSGTLRVGAQ 361 Query: 363 AQQVDGEWAVKKAIMSRSARVLMEGWVRVP 392 A DGEW V KA+MSRSARVLMEGWVRVP Sbjct: 362 ASLNDGEWVVTKAMMSRSARVLMEGWVRVP 391 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: 596 Number of extensions: 19 Number of successful extensions: 1 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: 394 Length adjustment: 31 Effective length of query: 365 Effective length of database: 363 Effective search space: 132495 Effective search space used: 132495 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