Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate BWI76_RS01660 BWI76_RS01660 malate synthase A
Query= SwissProt::Q10663 (968 letters) >FitnessBrowser__Koxy:BWI76_RS01660 Length = 533 Score = 494 bits (1273), Expect = e-144 Identities = 265/514 (51%), Positives = 338/514 (65%), Gaps = 11/514 (2%) Query: 453 DEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGW 512 +++ILTP+A+ FL +L + F P R RLL+ R Q Q I++ PDF ET +R+ + W Sbjct: 21 EKQILTPEAVEFLTELVSRFTPERNRLLAARIQQQQAIDDGK-LPDFISETASIRNSE-W 78 Query: 513 KGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYD 572 K IP DLQDRRVEITGP +RKMVINA+N+ VFMADFEDS +P W ++GQINL D Sbjct: 79 KIRGIPEDLQDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPEWNKVIDGQINLRD 138 Query: 573 AVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFH 632 AV ISYT+ K Y L A+L R RG HLPEKHV + GSLFDF L+ FH Sbjct: 139 AVNGTISYTNEAGKI-YQLKPNPALLICRVRGLHLPEKHVTWRGEAIPGSLFDFALYFFH 197 Query: 633 NAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQ 692 N KAL+ +GSGPYFYLPK Q+ +EA W++VF +TED+ L RGT+K T+LIE L A FQ Sbjct: 198 NYKALLEKGSGPYFYLPKTQAWQEAAWWSEVFSFTEDRFELPRGTVKATLLIETLPAVFQ 257 Query: 693 LHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVIK 752 + EI+HAL+D+IVGLNCGRWDYIFSYIKT +NH +LPDR + M PF+ YS +IK Sbjct: 258 MDEILHALRDHIVGLNCGRWDYIFSYIKTLKNHPDRVLPDRQVVTMDKPFLSAYSRLLIK 317 Query: 753 ACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAK 812 CH RG AMGGMAA IP K D N++ V+ADK EA +GHDGTW+AHPGL A Sbjct: 318 TCHKRGAFAMGGMAAFIPSK-DAERNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAM 376 Query: 813 RVFDQMMPKPNQISKNLTR---ANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRG 869 VF+ ++ + N+ ++TR A T E L EG RTE G R NI V + Y+++W+ G Sbjct: 377 AVFNGVLGE-NKNQLSVTREDDAPITAEQLLAPCEGERTEEGMRANIRVAVQYIEAWISG 435 Query: 870 TGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAE---TERRLI 926 GCVP+Y LMEDAATAEISR +WQW+HH+ L +G + L +Q +A E + L Sbjct: 436 NGCVPIYGLMEDAATAEISRTSIWQWIHHEKTLSNGTPVTKALFRQWLAEEMRVIQDELG 495 Query: 927 RAGSVVNRIPEAADLLEKFVTEEKMSDFLTTDAY 960 R EAA L+E+ T +++ DFLT Y Sbjct: 496 EHRYSSGRFDEAARLMEQITTSDELIDFLTLPGY 529 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: 1190 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: 533 Length adjustment: 40 Effective length of query: 928 Effective length of database: 493 Effective search space: 457504 Effective search space used: 457504 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