Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Pf6N2E2_1497 D-2-hydroxyglutarate dehydrogenase
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1497 Length = 474 Score = 167 bits (423), Expect = 7e-46 Identities = 139/454 (30%), Positives = 205/454 (45%), Gaps = 30/454 (6%) Query: 39 EDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPL 98 E+ PY D Y + V P E+V +++ C PVV +G TGL GGA P Sbjct: 22 EEAAPYLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAAADTPVVVQGGNTGLMGGATPD 81 Query: 99 EQG--ILLVMARFNKILEVDPAGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSI 156 G +LL++ R N++ VD V+ G + A + ++ +C++ Sbjct: 82 ASGRAVLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAGRLFPLSLGAEGSCTL 141 Query: 157 GGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMT-LGSDALDSPGFDLLALFTGSEG 215 GGN+ NAGG L+YG T L ++++T +GE L D+ G+DL LF GSEG Sbjct: 142 GGNLGTNAGGTAVLRYGNTRELTLGLEVVTAQGEIWNGLRGLRKDNTGYDLRDLFIGSEG 201 Query: 216 MLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRA- 274 LGI+T T+KL P P+ L AFDS+E+A + A L + LS Sbjct: 202 TLGIITAATLKLFPLPKARATALLAFDSLEQAVALLSHARAG--FGASLTAFELLSAECL 259 Query: 275 ---AEDFIHAGYPVDAEA---ILLCELDGVEADVHDDCARVSEVLK--LAGATEVRL--- 323 E F P L EL +D H + +R EV + L A E +L Sbjct: 260 ALLREQFPDGPRPFSGTRWPWFALLEL----SDNHSE-SRAREVFEQVLGEAFEQQLLAD 314 Query: 324 ---AKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKGISDLSEQF--G 378 A++ + FW R+N A R + D ++P ++ + L +Q G Sbjct: 315 ALIAENLVQSQAFWQLRENMSDAQKRAGRNMK-HDISVPISQVVAFVAHTDALLQQHFPG 373 Query: 379 LRVANVFHAGDGNMHPLIL--FDANQPGELERAEDLGGKILELCVKVGGSITGEHGVGRE 436 +R H GDGN+H + D+ + L + + GGSI+ EHG+G+ Sbjct: 374 VRHYTFGHLGDGNLHYNVAHPLDSTVDAHMAHYPALSQLVHDSAHAHGGSISAEHGIGQR 433 Query: 437 KINQMCSQFNADELTLFHAVKAAFDPSGLLNPGK 470 K+N + +A EL L H +K A DP LLNPGK Sbjct: 434 KVNVLGRYKSAVELDLMHRIKQALDPRNLLNPGK 467 Lambda K H 0.320 0.140 0.412 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: 496 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 474 Length adjustment: 34 Effective length of query: 465 Effective length of database: 440 Effective search space: 204600 Effective search space used: 204600 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: 52 (24.6 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