Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_027459094.1 K420_RS0116935 malate synthase A
Query= SwissProt::Q10663 (968 letters) >NCBI__GCF_000519045.1:WP_027459094.1 Length = 532 Score = 489 bits (1260), Expect = e-142 Identities = 257/515 (49%), Positives = 341/515 (66%), Gaps = 8/515 (1%) Query: 454 EKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGWK 513 E ILT +AL F+ L+ F RR LL R + QA I+ PDF ET+ +R WK Sbjct: 20 ESILTTEALEFVAKLHRAFEGRRQELLKARVERQARIDAGE-MPDFLPETKHIREGD-WK 77 Query: 514 GAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYDA 573 A IP LQ RRVEITGP + KM+INA NSGA+ +M DFEDSNSP W NQ++GQ+NLY A Sbjct: 78 VAPIPAALQCRRVEITGPVEAKMIINAFNSGADSYMTDFEDSNSPNWENQIQGQVNLYKA 137 Query: 574 VRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFHN 633 +R +S+ + K EY LN+K A L++RPRGWHL EKHVL+ Q SG LFDFGL FHN Sbjct: 138 IRRELSFKNEAGK-EYKLNDKIATLQIRPRGWHLDEKHVLVDGQRVSGGLFDFGLVFFHN 196 Query: 634 AKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQL 693 AK IA+G+GP++YLPK++S EA+LW D F +D G+ +GTIK TVL+E +LA+F++ Sbjct: 197 AKEQIARGAGPFYYLPKMESHLEARLWNDAFVMAQDHCGIPQGTIKATVLVETILATFEM 256 Query: 694 HEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVIKA 753 EI++ L+++ GLN GRWDYIFS IK F+ ++ F L R I M PFMR Y+L +++A Sbjct: 257 EEILYELRNHSAGLNAGRWDYIFSCIKKFKKNKDFCLAQRGAITMEVPFMRGYALALVQA 316 Query: 754 CHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAKR 813 CH RG AMGGM+A IPIK+D VAN+KA A +R DK R+A DG DG WVAHPGLVP+A Sbjct: 317 CHKRGAPAMGGMSALIPIKNDPVANEKALAGIRHDKTRDANDGFDGGWVAHPGLVPIAME 376 Query: 814 VFDQMM-PKPNQISKNLTRANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGTGC 872 F +++ KPNQ K + ++ L P TEAG R+NI+V + YL SWL G GC Sbjct: 377 EFVKVLGDKPNQFEKQVEGKFGPEQWLDFRPTTPITEAGLRNNINVGIHYLGSWLAGNGC 436 Query: 873 VPLYNLMEDAATAEISRAQLWQW-LHHDAKLEDGRTIDAGLVKQTIA---AETERRLIRA 928 VP++NLMEDAATAEISR+Q+WQW + L+DGR + +V+ IA A+ + + Sbjct: 437 VPIHNLMEDAATAEISRSQVWQWVVSPKGILDDGRKVTVEMVRPMIAEELAKVKATVTAQ 496 Query: 929 GSVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963 G +AA++ ++ +FLT Y+ + Sbjct: 497 GEDTATYDQAAEIFDRMSLTPDYPEFLTLPLYEAM 531 Lambda K H 0.319 0.134 0.402 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: 1251 Number of extensions: 57 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: 968 Length of database: 532 Length adjustment: 40 Effective length of query: 928 Effective length of database: 492 Effective search space: 456576 Effective search space used: 456576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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