Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate 6938261 Sama_2381 malate synthase (RefSeq)
Query= SwissProt::Q10663 (968 letters) >FitnessBrowser__SB2B:6938261 Length = 543 Score = 483 bits (1242), Expect = e-140 Identities = 260/530 (49%), Positives = 330/530 (62%), Gaps = 9/530 (1%) Query: 443 LSLTAQNVAGDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKE 502 L L ++ G E++ T A+ L L F LL+KR + Q I+ PDF E Sbjct: 15 LKLAGHHIQGQEEVFTEGAMSLLESLCARFAGDVDALLAKRKERQVRIDKGE-LPDFLPE 73 Query: 503 TEVLRSDQGWKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRN 562 T +R D W IP DLQDRRVEITGP DRKM+INA+N+ VFMADFEDS +P+W Sbjct: 74 TRAIR-DGKWTIRGIPTDLQDRRVEITGPVDRKMIINALNADVKVFMADFEDSLAPSWEK 132 Query: 563 QLEGQINLYDAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGS 622 ++GQINL DAVR I Y P T KEY LN+ AVL R RG HL EKHV + Q G+ Sbjct: 133 VIQGQINLRDAVRGTIEYKAPDTGKEYRLNDNPAVLIARVRGLHLKEKHVEFNGQSIPGA 192 Query: 623 LFDFGLFVFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTV 682 LFDF + +HN + L+++GSGPYFY+PKL+S EA+ WA VF +TE++ L GTIKCT Sbjct: 193 LFDFCFYFYHNYRQLLSKGSGPYFYIPKLESHLEARWWAKVFAFTEERFCLEPGTIKCTC 252 Query: 683 LIEHLLASFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPF 742 LIE L A F++ EI++ L+ NIV LNCGRWDYIFSYIKT ++H +LPDR Q+ M PF Sbjct: 253 LIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKTLKHHSDRVLPDRQQVTMDKPF 312 Query: 743 MRNYSLEVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWV 802 + YS +IK CH RG AMGGMAA IP K D AN V DKE EA +GHDGTWV Sbjct: 313 LSAYSRLLIKTCHKRGALAMGGMAAFIPAK-DAEANRLVLERVCKDKELEARNGHDGTWV 371 Query: 803 AHPGLVPLAKRVFDQMMPKPNQISKNLTR---ANCTKEDLTVIPEGTRTEAGFRHNISVT 859 AHPGL A VF+Q + + ++TR A +L EG RTE G R NI + Sbjct: 372 AHPGLAQTAMAVFNQFIGDDHCNQLHITRDVDAPILASELLAPCEGERTEHGMRLNIRIA 431 Query: 860 LGYLDSWLRGTGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAA 919 L Y+++W+ G GCVP+Y LMEDAATAEISRA +WQW+HH L +G+ + L+K+ + Sbjct: 432 LQYIEAWISGNGCVPIYGLMEDAATAEISRASIWQWIHHQKHLSNGKLVTKALLKEMLVE 491 Query: 920 ETERRLIRAGS---VVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRLVSE 966 E GS R +AA LLE+ T +++ DFLT Y+ L + Sbjct: 492 ELANVKEEVGSERFTHGRFTQAAVLLEEITTADELVDFLTLPGYELLTKQ 541 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: 1152 Number of extensions: 35 Number of successful extensions: 5 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: 543 Length adjustment: 40 Effective length of query: 928 Effective length of database: 503 Effective search space: 466784 Effective search space used: 466784 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 09 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