Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate RR42_RS11275 RR42_RS11275 3-methylitaconate isomerase
Query= SwissProt::Q937N7 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS11275 Length = 396 Score = 714 bits (1842), Expect = 0.0 Identities = 357/396 (90%), Positives = 373/396 (94%) Query: 1 MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60 M HVPQIKIPATYIRGGTSKGVFFRLQDLPE AQVPG ARDALLMRVIGSPDPYGKQIDG Sbjct: 1 MAHVPQIKIPATYIRGGTSKGVFFRLQDLPEAAQVPGAARDALLMRVIGSPDPYGKQIDG 60 Query: 61 MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 MGAATSSTSKTVILSKS++PDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL Sbjct: 61 MGAATSSTSKTVILSKSSKPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180 VD SRIPHNGVA+VRIWQANIGKTIIGHVP+TNG VQETGDFELDGVTFPAAEVQLEFMD Sbjct: 121 VDPSRIPHNGVAIVRIWQANIGKTIIGHVPITNGAVQETGDFELDGVTFPAAEVQLEFMD 180 Query: 181 PAAEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAI 240 PAAEE+GAGGAMFPTGN++DDLEVP VGTLKATMINAGIPTIF++AESIGY GTELQDAI Sbjct: 181 PAAEEDGAGGAMFPTGNLIDDLEVPGVGTLKATMINAGIPTIFLDAESIGYKGTELQDAI 240 Query: 241 NSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAAD 300 N D +ALAMFE +GA+RMGLIK++DEAA RQHTPKVAFV + DYVASSGK+VAA D Sbjct: 241 NGDPKALAMFETIRAHGAVRMGLIKHIDEAATRQHTPKVAFVAKPADYVASSGKQVAAGD 300 Query: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVG 360 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAI GTLVNLAAGGG RNAVRFGHPSGTLRVG Sbjct: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAITGTLVNLAAGGGARNAVRFGHPSGTLRVG 360 Query: 361 AEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396 AEA QVDGEW V KAIMSRSARVLMEGWVRVPGDAF Sbjct: 361 AEASQVDGEWTVTKAIMSRSARVLMEGWVRVPGDAF 396 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: 639 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: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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