Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Pf1N1B4_5862 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5862 Length = 499 Score = 172 bits (435), Expect = 3e-47 Identities = 138/460 (30%), Positives = 209/460 (45%), Gaps = 14/460 (3%) Query: 67 LAAFERIVPG-GVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLA 125 L A ++ VP ++ E L+ D L R ++ PR E+V +L+ CH RN+ Sbjct: 22 LKALQQEVPDLDILWREEELKPYECDGLSAYRTTPMLVALPRQLEQVQALLKLCHARNVP 81 Query: 126 VNPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERD 185 V +G TG+ GG++P+ ++L R N +L + Q G +S+ Sbjct: 82 VVARGAGTGLSGGALPLDKGVLLVMVRFNNILHIDPAARTARVQPGVRNLAISQAAAPFG 141 Query: 186 FIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKD 245 D ++ +C IGGNVA NAGG+ L+YG +L LEV+ +G L L + D Sbjct: 142 LYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKLEVLTLEGEHL-TLGADSLD 200 Query: 246 NTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGE 305 G+DL LF GSEG LGIIT V++ PKP+ V + +T + G Sbjct: 201 APGFDLLALFTGSEGLLGIITEVTVKLLPKPQVAKVLLASFDSVEKAGRTVAEIIA-AGI 259 Query: 306 ILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAG--HDAEKLGHFLEHALG 363 I E MD + ++ +H PV ++ +L E G A D E++ L+ A Sbjct: 260 IPGGLEMMDNLAIRAAEDFIHAGYPV-DAEAILLCELDGVEADVHDDCERVREVLQQAGA 318 Query: 364 SGLVTDGTMATDQRKVKMLWALRERITEALSR-DGYVYKYDLSLPVERLYDIVTDLRARL 422 S D A D+ + WA R+ A+ R Y D ++P L ++ + + Sbjct: 319 S----DVRQARDEAERVRFWAGRKNAFPAIGRLSPDYYCMDGTIPRRELPGVLKGIASLA 374 Query: 423 GPHAKHVVGYGHLGDGNLHLNVTAEAFSPSLL---AALEPHVYEWTAGQQGSVSAEHGVG 479 + V H GDGN+H + +A P L AL + E GS++ EHGVG Sbjct: 375 QEYGLRVANVFHAGDGNMHPLILFDANQPGELERAEALGGKILELCVKVGGSITGEHGVG 434 Query: 480 FRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTLPS 519 K + + L L +KA DPKG+LNP K +P+ Sbjct: 435 REKINQMCAQFNSDELTLFHAVKAAFDPKGLLNPGKNIPT 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: 641 Number of extensions: 24 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