Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_005458424.1 SACCYDRAFT_RS18190 malate synthase A
Query= SwissProt::Q10663 (968 letters) >NCBI__GCF_000244975.1:WP_005458424.1 Length = 534 Score = 489 bits (1258), Expect = e-142 Identities = 254/516 (49%), Positives = 340/516 (65%), Gaps = 8/516 (1%) Query: 454 EKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGWK 513 ++ILTP AL F+ L+ F RR LL R + + + F ET +R D+ W+ Sbjct: 20 DEILTPAALEFVAKLDNAFAGRRRELLDARRLRRERLASGEETLGFLPETRWIRGDESWQ 79 Query: 514 GAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYDA 573 A+ L+DRRVEITGP ++KM +NA+NSGA V++ADFED+ SPTW N + GQ+NLYDA Sbjct: 80 VAQPAPGLEDRRVEITGPPEKKMTVNALNSGAKVWLADFEDATSPTWHNIVSGQLNLYDA 139 Query: 574 VRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFHN 633 +R +I +T K Y + E+ A + RPRGWHL EKHV I +P S SL DFGL+ FHN Sbjct: 140 IRRDIDFTD--RGKRYVIGEEPATIVARPRGWHLVEKHVRIDGRPVSASLVDFGLYFFHN 197 Query: 634 AKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQL 693 A+ L+A+GSGPYFYLPKL+S EA+LW DVF++ +D+LG+ RGTI+ TVLIE + A+F++ Sbjct: 198 ARQLLARGSGPYFYLPKLESHHEARLWNDVFRFAQDELGIPRGTIRATVLIETITAAFEM 257 Query: 694 HEIIHALKDNIVGLNCGRWDYIFSYIKTFQNH-RKFLLPDRFQIGMTAPFMRNYSLEVIK 752 EI++ L+++ GLN GRWDYIFS IKTF +H ++LPDR Q+ MT PFMR Y+ +++ Sbjct: 258 DEILYELREHAAGLNAGRWDYIFSIIKTFASHGADYVLPDRVQVTMTVPFMRAYTELLVR 317 Query: 753 ACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAK 812 CH RG HA+GGMAA IP + +V N A VR DKEREA DG DG+WVAHPGLVP+ + Sbjct: 318 TCHKRGAHAIGGMAAFIPSRDPEV-NATALEKVRQDKEREAGDGFDGSWVAHPGLVPVCR 376 Query: 813 RVFDQMMPK-PNQISKNLTRANCTKEDLTVIPE--GTRTEAGFRHNISVTLGYLDSWLRG 869 FD+++ PNQ+ + T EDL + G TE G R NI+V L Y+D+WLRG Sbjct: 377 EAFDEVLGGWPNQLGRLREDVVVTAEDLLNVASAGGEVTEQGVRSNINVALRYVDAWLRG 436 Query: 870 TGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRLIRAG 929 TG ++ LMEDAATAEI+R Q+WQW+ + KL DG I V + AE G Sbjct: 437 TGAAAIFGLMEDAATAEIARCQVWQWVRNGTKLADGTAITPERVMDWLDAELAGVHAELG 496 Query: 930 SVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRLVS 965 NR+ EA ++L + EK+ F TT AY R ++ Sbjct: 497 E-GNRLTEAREILVETALSEKLPSFFTTGAYARYLT 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: 1199 Number of extensions: 41 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: 534 Length adjustment: 40 Effective length of query: 928 Effective length of database: 494 Effective search space: 458432 Effective search space used: 458432 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