Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate HSERO_RS19115 HSERO_RS19115 D-lactate dehydrogenase
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__HerbieS:HSERO_RS19115 Length = 471 Score = 178 bits (451), Expect = 4e-49 Identities = 126/420 (30%), Positives = 200/420 (47%), Gaps = 22/420 (5%) Query: 108 TSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGILV 167 ++EEV+ ++ C + + + P G T + G + + + + ++MN+VL+ H+ Sbjct: 60 STEEVAAFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVHAEDLTAT 119 Query: 168 CQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLE 227 QAG ++L++ +++ P+D GA S +GG +T A G +RYG++ L L Sbjct: 120 VQAGVTRKQLNQEIKDTGLFFPIDPGADAS--LGGMASTRASGTNAVRYGTMKENTLTLT 177 Query: 228 VVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCP 287 VV A G ++ T +K + GYDL ++++GSEGTLGIIT V++ P+P A++ A P Sbjct: 178 VVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFP 237 Query: 288 GFAEVLQTFSTCKGMLGEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNA 347 A+ + T M G L+ E +D ++ + H L+ PV +L E GS Sbjct: 238 TVADAVNTVIQTIQM-GVPLARVELLDENGVRAINAHDKLSLPVNP---LLLFEFHGSEN 293 Query: 348 G--HDAEKLGHFLE--HALGSGLVTDGTMATDQRKVKMLWALRERITEALSR---DGYVY 400 G AE + + HALG AT LW R AL + Sbjct: 294 GVKEQAELVQDIAKEFHALGF------EWATRPEDRTRLWTARHNAYFALLQLRPGARAI 347 Query: 401 KYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSLLAALE-- 458 D +P+ RL + V +A GH+GDGN H+ + + P+ +A E Sbjct: 348 STDCCVPISRLAECVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGV 407 Query: 459 -PHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517 + G G+ + EHGVG K D L GA+ +M+ +K LDPK I+NP K L Sbjct: 408 NQRMVARAIGMDGTCTGEHGVGLHKMDFLIQEHGEGAIAVMRAIKHALDPKNIMNPGKIL 467 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: 580 Number of extensions: 24 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: 471 Length adjustment: 34 Effective length of query: 487 Effective length of database: 437 Effective search space: 212819 Effective search space used: 212819 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