Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate 200654 SO1483 malate synthase A (NCBI ptt file)
Query= SwissProt::Q10663 (968 letters) >FitnessBrowser__MR1:200654 Length = 549 Score = 483 bits (1243), Expect = e-140 Identities = 260/529 (49%), Positives = 326/529 (61%), Gaps = 9/529 (1%) Query: 443 LSLTAQNVAGDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKE 502 L+L + G E I T A+ L L EF LL+KR QA I+ PDF E Sbjct: 24 LALVGNTIPGQEVIFTEGAMALLESLCREFGAEVPTLLAKRKDRQARIDKGA-LPDFLPE 82 Query: 503 TEVLRSDQGWKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRN 562 T +R D WK IP DL DRRVEITGP +RKMVINA+N+ A VFMADFEDS +P+W+ Sbjct: 83 TRAIR-DGAWKIRGIPNDLLDRRVEITGPVERKMVINALNANAKVFMADFEDSLAPSWQK 141 Query: 563 QLEGQINLYDAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGS 622 +EGQINL DAVR I YT P T K Y L AVL R RG HL EKHV + Q G Sbjct: 142 VVEGQINLRDAVRGEIEYTAPETGKHYKLGPNPAVLICRVRGLHLKEKHVEFNQQSIPGG 201 Query: 623 LFDFGLFVFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTV 682 LFDF ++ +HN + L+A+GSGPYFY+PKL+S EA+ WA VF + E++ L GTIKCT Sbjct: 202 LFDFAMYFYHNYRQLLAKGSGPYFYIPKLESHIEARWWAKVFAFVEERFCLQAGTIKCTC 261 Query: 683 LIEHLLASFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPF 742 LIE L A F++ EI++ L+ NIV LNCGRWDYIFSYIKT + H +LPDR + M PF Sbjct: 262 LIETLPAVFEMDEILYELRSNIVALNCGRWDYIFSYIKTLKRHGDRVLPDRQAVTMDTPF 321 Query: 743 MRNYSLEVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWV 802 + YS +IK CH RG AMGGMAA IP K D N+ VR DKE EA +GHDGTWV Sbjct: 322 LSAYSRLLIKTCHKRGALAMGGMAAFIPAK-DPAQNEAVLQRVRKDKELEARNGHDGTWV 380 Query: 803 AHPGLVPLAKRVFDQMMPKPNQISKNLTR---ANCTKEDLTVIPEGTRTEAGFRHNISVT 859 AHPGL A +F++ + + +Q ++TR A +L +G RTE G R NI + Sbjct: 381 AHPGLADTAMGIFNEYIGQDHQNQLHITRDVDAPILAAELLKTCDGERTEQGMRLNIRIA 440 Query: 860 LGYLDSWLRGTGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAA 919 L YL++W+ G GCVP+Y LMEDAATAEISRA +WQW+ H L +G+ + L K + Sbjct: 441 LQYLEAWISGNGCVPIYGLMEDAATAEISRASIWQWIQHGKSLSNGKLVTKQLFKDMLVE 500 Query: 920 ETERRLIRAGS---VVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRLVS 965 E GS + +AA LLE T +++ DFLT Y+ L + Sbjct: 501 ELANVKKEVGSDRFTHGKFTQAAVLLEDITTSDELVDFLTLPGYEMLTA 549 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: 1170 Number of extensions: 41 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: 549 Length adjustment: 40 Effective length of query: 928 Effective length of database: 509 Effective search space: 472352 Effective search space used: 472352 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