Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate BPHYT_RS12305 BPHYT_RS12305 malate synthase
Query= SwissProt::Q10663 (968 letters) >FitnessBrowser__BFirm:BPHYT_RS12305 Length = 536 Score = 509 bits (1311), Expect = e-148 Identities = 269/524 (51%), Positives = 354/524 (67%), Gaps = 7/524 (1%) Query: 443 LSLTAQNVAGDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKE 502 + +TA+ G + IL+ +AL + L+ F PRR +LL R + ++ PDF E Sbjct: 17 MEITAEIKPGYDAILSREALELVAALHRTFEPRRQQLLQARAERTKRLDAGER-PDFLAE 75 Query: 503 TEVLRSDQGWKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRN 562 T+ +R D W A +P+DLQ RRVEITGP +RKM+INA+NSGA+ +M DFEDSN+P+W N Sbjct: 76 TKSVR-DGDWTIAPLPQDLQCRRVEITGPVERKMIINALNSGADSYMTDFEDSNAPSWDN 134 Query: 563 QLEGQINLYDAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGS 622 Q+ G INL DAVR IS K YTLN+K A L VRPRGWHL EKHV + + SG Sbjct: 135 QITGHINLKDAVRRTISLEQ--NGKSYTLNDKVATLIVRPRGWHLDEKHVKVDGKRVSGG 192 Query: 623 LFDFGLFVFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTV 682 +FDF LF+ HNAK L+A+GSGPYFYLPK++S EA+LW D+F ++ +G+ RGTI+ TV Sbjct: 193 IFDFALFMVHNAKELVARGSGPYFYLPKMESHLEARLWNDIFVAAQEAVGVPRGTIRATV 252 Query: 683 LIEHLLASFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPF 742 LIE ++A+F++ EI++ L+++ GLN GRWDYIFS IK F+ R F L DR QI MT+PF Sbjct: 253 LIETIVAAFEMDEILYELREHSSGLNAGRWDYIFSAIKKFKADRDFCLADRSQITMTSPF 312 Query: 743 MRNYSLEVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWV 802 MR Y+L ++K CH R A+GGM+A IPIK+D ANDKA + VR+DK R+A DG+DG WV Sbjct: 313 MRAYALLLLKTCHRRNAPAIGGMSALIPIKNDPAANDKAMSGVRSDKARDAGDGYDGGWV 372 Query: 803 AHPGLVPLAKRVFDQMM-PKPNQISKNLTRANCTKEDLTVI-PEGTRTEAGFRHNISVTL 860 AHPGLVP+A F +++ KPNQI K T DLT PE TE G R+NI+V + Sbjct: 373 AHPGLVPIAMEEFVKVLGDKPNQIGKQRDDVLVTATDLTDFRPEAPITEGGLRNNINVGI 432 Query: 861 GYLDSWLRGTGCVPLYNLMEDAATAEISRAQLWQWLHH-DAKLEDGRTIDAGLVKQTIAA 919 YL +WL G GCVP++NLMEDAATAEISR+Q+WQW+ KLEDGR + A LV++ A Sbjct: 433 HYLGAWLAGNGCVPIHNLMEDAATAEISRSQVWQWIRSPKGKLEDGRKVTAELVRELSAQ 492 Query: 920 ETERRLIRAGSVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963 E E+ G AA + E+ T E+ +DFLT Y+ + Sbjct: 493 ELEKVKQAVGGDTKPYERAAQIFEEMSTSEQFTDFLTLPLYEEI 536 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: 1143 Number of extensions: 42 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: 536 Length adjustment: 40 Effective length of query: 928 Effective length of database: 496 Effective search space: 460288 Effective search space used: 460288 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