Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Pf1N1B4_4264 Aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::Q9LES4 (483 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4264 Length = 399 Score = 341 bits (874), Expect = 3e-98 Identities = 187/432 (43%), Positives = 261/432 (60%), Gaps = 45/432 (10%) Query: 48 LKPTWNLI--NVVDASKTIVRGISGGAETIAKERVDTVVIGAGVVGLAVARELSLRGREV 105 ++ +W +I +++D + + G+ GG ++ ++ VV+GAGVVGLAVAR L+ GREV Sbjct: 1 MQSSWLVIFFSLIDYRERGLAGMGGGQVSVD---IECVVVGAGVVGLAVARALARIGREV 57 Query: 106 LILDAASSFGTVTSSRNSEVVHAGIYYPPNSLKAKFCVRGRELLYKYCSEYEIPHKKIGK 165 ++++A G SSRNSEV+HAGIYYP SLKA+ CV GR+ LY +C E + +++IGK Sbjct: 58 ILVEAGEGIGVGISSRNSEVIHAGIYYPSGSLKAQLCVEGRQRLYAFCDERGVDYRRIGK 117 Query: 166 LIVATGSSEIPKLDLLMHLGTQNRVSGLRMLEGFEAMRMEPQLRCVKALLSPESGILDTH 225 LIVAT + L L+ G +N V L+ L+ +A +EP L CV AL SP +GI+D+H Sbjct: 118 LIVATDDRQRHALQALLEQGRRNGVDDLQWLDAGQAQALEPALSCVAALWSPSTGIVDSH 177 Query: 226 SFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNHATFSYNTVVLNGRVEEKKMHLYVADTRF 285 + ML+ LQ +A+ + +++T + + R E L++ + Sbjct: 178 ALMLA------------------LQADAEACGTSIAFHTPLESARCTEHGFELHLGGAQP 219 Query: 286 SESRCEAEAQLELIPNLVVNSAGLGAQALAKRLHGLDHRFVPSSHYARGCYFTLSGIKAP 345 C ++N AGL A +A R+ GL + VP + +G YF+ SG Sbjct: 220 MPLSCRQ----------LINCAGLSAPDVASRIEGLPAQHVPKAWLCKGSYFSFSG--RA 267 Query: 346 PFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPDVEWIECTDDTSSFLNKFDYRVNPQRSEK 405 PF LVYP PE GLGVH+T+DL G +FGPDVEW+E + DYRV+P+RS Sbjct: 268 PFRHLVYPAPESAGLGVHMTLDLGGQARFGPDVEWVE----------QVDYRVDPRRSVS 317 Query: 406 FYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPKQSPADFVIQGEETHGVPGLVNLFGIESP 465 FY IR+Y+P L D SL+P YSGIRPK+SGP ADFVI + HGVPGLVNLFGIESP Sbjct: 318 FYQAIRRYWPALPDNSLQPAYSGIRPKISGPTGPAADFVISAPDVHGVPGLVNLFGIESP 377 Query: 466 GLTSSLAIAEHI 477 GLTS LA+A+ + Sbjct: 378 GLTSCLALADRV 389 Lambda K H 0.318 0.136 0.401 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: 524 Number of extensions: 23 Number of successful extensions: 4 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: 483 Length of database: 399 Length adjustment: 32 Effective length of query: 451 Effective length of database: 367 Effective search space: 165517 Effective search space used: 165517 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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