Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_089302434.1 CHB84_RS16050 malate synthase A
Query= SwissProt::Q10663 (968 letters) >NCBI__GCF_900188115.1:WP_089302434.1 Length = 525 Score = 457 bits (1176), Expect = e-133 Identities = 246/518 (47%), Positives = 333/518 (64%), Gaps = 13/518 (2%) Query: 452 GDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQG 511 GDE ILTP+AL F+ L+ F RR LL R + + + DF ET +RS Sbjct: 14 GDE-ILTPEALAFVGSLHEAFAARRDELLRARKTRRQEAARTGKM-DFLPETADVRSGD- 70 Query: 512 WKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLY 571 W+ AE P L+DRRVEITGPTDRKM INA+NSGA V++AD ED+N+P W N + GQ+NLY Sbjct: 71 WQVAEAPEALRDRRVEITGPTDRKMTINALNSGAKVWLADLEDANTPHWDNVVSGQVNLY 130 Query: 572 DAVRNNISYTHPTTKKEYTLNE--KHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLF 629 DA R + T +K YT+ +H + VRPRGWHLPE+++ I Q G+L DFGL Sbjct: 131 DAARKQVELH--TAEKSYTVRTDIEHPTVVVRPRGWHLPERNITIDGQQAIGALVDFGLH 188 Query: 630 VFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLA 689 FHNA L QG+GP++YLPKL+S EA+LW DVF + + +LG+ GT++ TVLIE + A Sbjct: 189 FFHNAAYLAEQGAGPFYYLPKLESHLEARLWNDVFTHAQAELGIPHGTVRATVLIETIPA 248 Query: 690 SFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTF-QNHRKFLLPDRFQIGMTAPFMRNYSL 748 +F++ EI++ L+D+ GLN GRWDY+FS IK F ++ +F LPDR + MTAPFMR Y+ Sbjct: 249 AFEMEEILYELRDHAAGLNAGRWDYLFSVIKYFRESGEEFTLPDRNAVTMTAPFMRAYTE 308 Query: 749 EVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLV 808 +++ CH RG A+GGMAA IP + D ++A A VR DK REA DG DG+WVAHP LV Sbjct: 309 LLVRTCHKRGAFAIGGMAAFIPNRRDPEVTERALAKVREDKNREAGDGFDGSWVAHPDLV 368 Query: 809 PLAKRVFDQMM-PKPNQISKNLTRANCTKEDLTVIPE--GTRTEAGFRHNISVTLGYLDS 865 P+ + +FD+++ KPNQ+ + + T E L + G RT G R I V L Y+ S Sbjct: 369 PVCREIFDEVLGDKPNQLDRTREDVSVTAEQLLEVASTPGGRTRDGLRGAIDVGLRYIAS 428 Query: 866 WLRGTGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRL 925 WL GTG ++NLMEDAATAEISR+Q+WQW+H L+ G + + LV++ + E L Sbjct: 429 WLGGTGAAAIHNLMEDAATAEISRSQVWQWVHGGIVLDTGEKVTSDLVRE-VLGEVRAEL 487 Query: 926 IRAGSVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963 N + AA+L E+ ++ DFLT AY+R+ Sbjct: 488 SEVID-ANLLEPAAELFEQVALADEFPDFLTLPAYERI 524 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: 1197 Number of extensions: 58 Number of successful extensions: 6 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: 525 Length adjustment: 39 Effective length of query: 929 Effective length of database: 486 Effective search space: 451494 Effective search space used: 451494 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