Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate 209326 DVU0390 glycolate oxidase, subunit GlcD, putative
Query= BRENDA::Q8N465 (521 letters) >MicrobesOnline__882:209326 Length = 460 Score = 191 bits (484), Expect = 6e-53 Identities = 132/432 (30%), Positives = 208/432 (48%), Gaps = 20/432 (4%) Query: 96 LRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNR 155 LR +++ P + ++ ++R E V P+GG TG+ GG + + ++LS RMNR Sbjct: 40 LRATPDMVVLPESVGQIQALMRLATEHRFPVIPRGGGTGLAGGCLALMGGVVLSVERMNR 99 Query: 156 VLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLR 215 V + + + + AGC+ + L + P D +GGNVATNAGG ++ Sbjct: 100 VRAIDTRNLVAEVDAGCITQTLRDAAAAANLFYPPDPAGMDRSTVGGNVATNAGGPACVK 159 Query: 216 YGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPK 275 YG VLG+E VL DG +L RK GYD+ L GSEGTLG+IT +++ P Sbjct: 160 YGVTRDYVLGVEAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGVITGLTMKLIPL 219 Query: 276 PRA---VNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDAVCMQLVGRHLHLASPVQ 332 P A + VAF P ++ + G G + SA EFMD C+ LVG L P Sbjct: 220 PAATVGMAVAFADMP---SAMRAVAAVLG-AGHLPSAIEFMDHRCLALVGEMLPFPVP-G 274 Query: 333 ESPFYVLIETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEA 392 P ++IE G A + + L G TD + +W +R +++ Sbjct: 275 ARPSLLIIELDGQRATIEPQ-LDAVAAICREQGATQVLPAPTDAERA-TIWGVRRQVSLR 332 Query: 393 L-SRDGYVYKYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAF-- 449 + G D+++P+ + D+V +L A + + +GH GDGN+HLNVT+ + Sbjct: 333 IHDYAGLYLSEDVAVPLVAIADLVAELPAFEERYGLEIFAFGHAGDGNIHLNVTSSSTDN 392 Query: 450 ---SPSLLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLD 506 + + AL V E G++S EHG+G K+ ++ ++ L + ++ + D Sbjct: 393 RERAEEGVVALARRVVE----LGGTISGEHGIGEAKKHLVPLELSARSIALQKGIRGVFD 448 Query: 507 PKGILNPYKTLP 518 P GI+NP K P Sbjct: 449 PLGIMNPGKVFP 460 Lambda K H 0.321 0.139 0.426 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: 638 Number of extensions: 36 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: 521 Length of database: 460 Length adjustment: 34 Effective length of query: 487 Effective length of database: 426 Effective search space: 207462 Effective search space used: 207462 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