Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate WP_093427929.1 BM272_RS06345 FAD-binding protein
Query= BRENDA::Q8N465 (521 letters) >NCBI__GCF_900112605.1:WP_093427929.1 Length = 462 Score = 203 bits (517), Expect = 1e-56 Identities = 143/451 (31%), Positives = 213/451 (47%), Gaps = 15/451 (3%) Query: 76 GGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGM 135 G ++TDP+ D R +G + +P ++V+ ILRHCH + V P+G TG Sbjct: 18 GALLTDPDECWVYGYDNSRR-QGRPVAVAQPEDRDQVAAILRHCHAAGVTVTPRGRGTGT 76 Query: 136 VGGSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAK 195 G +VP +ILST R+ R+ + +V + G + E F P D + Sbjct: 77 TGATVPDHGGVILSTERLRRLEPVAADDRYVVAEPGVTNGAVQAAAGEHGFFWPPDPTSA 136 Query: 196 GSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLF 255 C IGGN+A N+ G R ++YG+ LGLE V DG VL K GYDL +L Sbjct: 137 AYCSIGGNLAYNSAGPRAVKYGTPRENTLGLEAVTMDGRVLRSGVRTTKGVVGYDLTRLL 196 Query: 256 IGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDA 315 IGSEGTL +IT ++ P P A A + S + A EF+D Sbjct: 197 IGSEGTLAVITEATLKLTPLPEARATLKAVYADMAAAARAVSRIMAQ-PVVPCALEFIDG 255 Query: 316 VCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATD 375 +++V H P + + ++IE G A +A A G GL+ D AT+ Sbjct: 256 AAIEMVHSHSEADLP-EGAGALLMIEVDGPAACLEASATA-VANAAHGEGLL-DLQRATE 312 Query: 376 QRKVKMLWALRERITEALSRDG-YVYKYDLSLPVERLYDIVTDLRARLGPHAKHVVGYGH 434 V LWA R+ ++ AL + D+ +PV R+ +++ L+ H +V +GH Sbjct: 313 AADVAALWATRKALSPALRQVAPKKINEDVVVPVSRIPELIEGLQGLGRRHGITIVNFGH 372 Query: 435 LGDGNLHLNVTAEAFSPSLLAALE------PHVYEWTAGQQGSVSAEHGVGFRKRDVLGY 488 G+GN+H+N+ +P L+ V+ G G++S EHGVG KRD + Sbjct: 373 AGNGNIHVNLLV---NPDDAEELDRAWRCLDEVFALVLGLDGTLSGEHGVGLEKRDYVDR 429 Query: 489 SKPPGALQLMQQLKALLDPKGILNPYKTLPS 519 P L LM+ +K DP+G+LNP K LP+ Sbjct: 430 EITPATLDLMRGIKEAFDPRGLLNPGKGLPN 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: 618 Number of extensions: 31 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: 462 Length adjustment: 34 Effective length of query: 487 Effective length of database: 428 Effective search space: 208436 Effective search space used: 208436 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 24 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