Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate H281DRAFT_02982 H281DRAFT_02982 2-methylaconitate cis-trans isomerase
Query= SwissProt::Q937N7 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_02982 Length = 393 Score = 668 bits (1723), Expect = 0.0 Identities = 329/393 (83%), Positives = 361/393 (91%) Query: 1 MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60 M H PQI+IPATY+RGGTSKGVFFRLQDLP+ AQ PG ARDALL+RVIGSPDPYGKQIDG Sbjct: 1 MAHKPQIRIPATYMRGGTSKGVFFRLQDLPDAAQTPGAARDALLLRVIGSPDPYGKQIDG 60 Query: 61 MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 MG ATSSTSKTVI++KS++PDHDVDYLFGQVSID+PFVDWSGNCGNLSAAVGPFAISAGL Sbjct: 61 MGGATSSTSKTVIIAKSSKPDHDVDYLFGQVSIDKPFVDWSGNCGNLSAAVGPFAISAGL 120 Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180 V+A+RIP +GVA VRIWQANIGKTII HVP+++G VQETGDFELDGVTFPAAEVQLEFMD Sbjct: 121 VEANRIPRDGVATVRIWQANIGKTIIAHVPMSDGAVQETGDFELDGVTFPAAEVQLEFMD 180 Query: 181 PAAEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAI 240 PAAEE GAGG+MFPTGN+VDDL+VP VGTLKATMINAGIPTIFVNAE+IGY GTELQDAI Sbjct: 181 PAAEEAGAGGSMFPTGNLVDDLDVPGVGTLKATMINAGIPTIFVNAEAIGYKGTELQDAI 240 Query: 241 NSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAAD 300 NSD +ALAMFE +GALRMGLIK++DE A RQHTPK+AFV + DYV+SSGK++ + D Sbjct: 241 NSDEKALAMFETIRAHGALRMGLIKHLDEIATRQHTPKIAFVAKPADYVSSSGKRIGSGD 300 Query: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVG 360 DLLVRA+SMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGER AVRFGHPSGTLRVG Sbjct: 301 ADLLVRAMSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEREAVRFGHPSGTLRVG 360 Query: 361 AEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPG 393 AEA V GEW V+KA+MSRSARVLMEGWVRV G Sbjct: 361 AEAAVVGGEWVVRKAVMSRSARVLMEGWVRVQG 393 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: 17 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: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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