Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate PP_3745 PP_3745 glycolate oxidase, putative FAD-linked subunit
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__Putida:PP_3745 Length = 499 Score = 165 bits (418), Expect = 3e-45 Identities = 134/446 (30%), Positives = 208/446 (46%), Gaps = 19/446 (4%) Query: 83 EALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPV 142 E L+ D L R ++ P E+V +L+ CH+R + V +G TG+ GG++P+ Sbjct: 39 EDLKPYECDGLSAYRTVPLLVALPERLEQVQTLLKLCHQRGVPVVARGAGTGLSGGALPL 98 Query: 143 FDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGG 202 I+L AR NR+L + Q G +S+ D ++ +C IGG Sbjct: 99 AKGILLVMARFNRILEVNPQGRYARVQPGVRNLAISQAAAPHGMYYAPDPSSQIACSIGG 158 Query: 203 NVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTL 262 NVA NAGG+ L+YG VL ++++ +G L L S D+ G+DL LFIGSEG L Sbjct: 159 NVAENAGGVHCLKYGLTVHNVLKVDILTVEGERLS-LGSDALDSPGFDLLALFIGSEGML 217 Query: 263 GIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDAVCMQLVG 322 GI+T V++ PKP+ V + + + G I E MD + ++ Sbjct: 218 GIVTEVTVKLLPKPQVARVILASFDSVEDAGRAVADIIA-AGIIPGGLEMMDNLAIRAAE 276 Query: 323 RHLHLASPVQESPFYVLIETSGSNAG--HDAEKLGHFLEHALGSGLVTDGTMATDQRKVK 380 +H PV ++ +L E G A D E++ L A G+ V +A D+ + Sbjct: 277 DFIHAGYPV-DAAAILLCELDGVEADVYDDCERVAAVLTQA-GAREV---HLACDEAERA 331 Query: 381 MLWALRERITEALSR-DGYVYKYDLSLP---VERLYDIVTDLRARLGPHAKHVVGYGHLG 436 WA R+ A+ R Y D ++P + R+ ++DL A G +V H G Sbjct: 332 RFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPRVLKGISDLSAEYGLRVANVF---HAG 388 Query: 437 DGNLHLNVTAEAFSPSLL---AALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPG 493 DGN+H + +A P L A+ + E GS++ EHGVG K + + Sbjct: 389 DGNMHPLILFDANLPGELERAEAIGGKILELCVKVGGSITGEHGVGREKINQMCAQFNSD 448 Query: 494 ALQLMQQLKALLDPKGILNPYKTLPS 519 + L +KA DP+G+LNP K +P+ Sbjct: 449 EITLFHAVKAAFDPQGLLNPGKNIPT 474 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: 689 Number of extensions: 27 Number of successful extensions: 5 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: 499 Length adjustment: 34 Effective length of query: 487 Effective length of database: 465 Effective search space: 226455 Effective search space used: 226455 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