Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_057509261.1 ABB28_RS14270 malate synthase A
Query= SwissProt::Q10663 (968 letters) >NCBI__GCF_001431535.1:WP_057509261.1 Length = 545 Score = 507 bits (1306), Expect = e-148 Identities = 275/529 (51%), Positives = 344/529 (65%), Gaps = 11/529 (2%) Query: 443 LSLTAQNVAGDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKE 502 ++LT Q VAG +L L L L+ P R L+ R Q QA + PDF + Sbjct: 19 ITLTTQ-VAGQSALLPAPLLALLVSLHRAVEPGRQARLAARVQRQAFFDQG-GLPDFRTD 76 Query: 503 TEVLRSDQGWKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRN 562 T +R++ WK A +P L DRRVEITGPTD KMVINA+NSGA VFMADFED+ +PTW N Sbjct: 77 TAPIRAED-WKVAPLPAALLDRRVEITGPTDPKMVINALNSGAKVFMADFEDATAPTWGN 135 Query: 563 QLEGQINLYDAVRNNISYTHPTT----KKEYTLN--EKHAVLKVRPRGWHLPEKHVLIHN 616 L GQ +L AVR ++ +T P + K Y+L E+ AVL VRPRGWHL EKHVL+ Sbjct: 136 LLAGQQSLIGAVRGDLQFTAPASGSKPSKHYSLRPYEERAVLIVRPRGWHLDEKHVLVDG 195 Query: 617 QPTSGSLFDFGLFVFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARG 676 Q +G LFD +F +HNA+ L+A GPYFYLPKLQS EEA LW + E LGL G Sbjct: 196 QRLAGGLFDAAVFAYHNARTLMANDRGPYFYLPKLQSMEEAALWETALSHIEGMLGLPHG 255 Query: 677 TIKCTVLIEHLLASFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQI 736 IK TVLIE L A F++ EI+HAL+D IVGLNCGRWDYIFSY+KTF+ H +LP+R Q+ Sbjct: 256 QIKVTVLIETLPAVFEMDEILHALRDRIVGLNCGRWDYIFSYLKTFRRHADKVLPERGQV 315 Query: 737 GMTAPFMRNYSLEVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDG 796 MT PF++ YS +I+ CH RG HAMGGMAAQIPI +D AN++A A VRADK RE T G Sbjct: 316 TMTQPFLKAYSELLIQTCHRRGAHAMGGMAAQIPIGNDAAANEQAMARVRADKLREVTAG 375 Query: 797 HDGTWVAHPGLVPLAKRVFDQMMPKPNQISKNLTRANCTKEDLTVIPEGTRTEAGFRHNI 856 HDGTWVAHP L+P+A +FD+ MP NQ ++ L P G+ + AGF N+ Sbjct: 376 HDGTWVAHPALIPVAMAIFDEHMPGANQQQVLRQDVRVDRDQLIARPPGSISRAGFEGNV 435 Query: 857 SVTLGYLDSWLRGTGCVPLYNLMEDAATAEISRAQLWQWLHHDA-KLEDGRTIDAGLVKQ 915 V + YL +WL G GCVP++NLMEDAATAEISR+QLWQWLH +L+DG IDA L+ Sbjct: 436 EVCVRYLAAWLDGNGCVPIHNLMEDAATAEISRSQLWQWLHTPGQQLDDGTAIDAALLDN 495 Query: 916 TIAAETERRLIRAG-SVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963 +A R RA R+ EA LL + ++++DFLT AY R+ Sbjct: 496 ALAQLPARLGDRATLPGGGRVDEAIALLAELSRADELNDFLTLPAYARI 544 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: 1165 Number of extensions: 41 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: 545 Length adjustment: 40 Effective length of query: 928 Effective length of database: 505 Effective search space: 468640 Effective search space used: 468640 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