Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate AZOBR_RS24310 AZOBR_RS24310 3-methylitaconate isomerase
Query= SwissProt::Q937N7 (396 letters) >FitnessBrowser__azobra:AZOBR_RS24310 Length = 401 Score = 575 bits (1483), Expect = e-169 Identities = 294/401 (73%), Positives = 321/401 (80%), Gaps = 5/401 (1%) Query: 1 MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60 M PQI+IPATY+RGGTSKGVFFRL DLPE +VPG ARD L +RVIGSPDPY K IDG Sbjct: 1 MAFAPQIRIPATYMRGGTSKGVFFRLDDLPERCRVPGEARDRLFLRVIGSPDPYAKHIDG 60 Query: 61 MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120 MG A+SSTSK VILSKS RP HDVDYL+GQV+ID FVDWSGNCGNLS A G FAI AGL Sbjct: 61 MGGASSSTSKCVILSKSARPGHDVDYLYGQVAIDAAFVDWSGNCGNLSTAAGAFAIHAGL 120 Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180 VD +R+P NGV VRIWQANIGKTII HVPVT G+VQETG F LDGVTFPAAE+ LEF+D Sbjct: 121 VDPARVPENGVCTVRIWQANIGKTIIAHVPVTAGQVQETGSFALDGVTFPAAEIVLEFID 180 Query: 181 PAAE-EEGAGGAMFPTGNVVDDLEVP----AVGTLKATMINAGIPTIFVNAESIGYTGTE 235 PA E E GG+M PTGN +DDL+VP G LKAT+INAGIPTIF++A +GY GTE Sbjct: 181 PADEGESEGGGSMLPTGNPIDDLDVPDSLVPGGRLKATLINAGIPTIFIDAADLGYRGTE 240 Query: 236 LQDAINSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKK 295 Q AIN D ALA FE GALRMGLI+ EAA+RQHTPK+AFV Y ASSGK+ Sbjct: 241 SQAAINGDATALARFEALRTIGALRMGLIREPGEAARRQHTPKIAFVAPPDAYTASSGKR 300 Query: 296 VAAADVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSG 355 V A D+DLLVRALSMGKLHHAMMGTA+VAI AAA+PGTLVN AAGGG RNAVRFGHPSG Sbjct: 301 VEAGDIDLLVRALSMGKLHHAMMGTASVAIAAAAAVPGTLVNRAAGGGTRNAVRFGHPSG 360 Query: 356 TLRVGAEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396 TLRVGAEA VDG W V KAIMSRSARVLMEGWV VP D+F Sbjct: 361 TLRVGAEAALVDGRWTVTKAIMSRSARVLMEGWVCVPADSF 401 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: 548 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: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 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