Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate BPHYT_RS32905 BPHYT_RS32905 FAD-linked oxidase
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__BFirm:BPHYT_RS32905 Length = 463 Score = 308 bits (790), Expect = 2e-88 Identities = 186/438 (42%), Positives = 242/438 (55%), Gaps = 5/438 (1%) Query: 78 VVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVG 137 V D +A DW R ++ L PR E+V+ LR E AV QGG TG+ G Sbjct: 22 VSLDAAVAEAHAGDWSDAPRMRPRMTLLPRNPEDVARALRVLGEHRQAVVVQGGLTGLAG 81 Query: 138 GSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGS 197 G+ P E+ LS AR+N + SF + G L QAG LE+L +VE + PLDLGA+G+ Sbjct: 82 GATPQAGEVALSLARVNAIESFDRIGGTLTVQAGVPLEQLQTFVEAEGWFFPLDLGARGT 141 Query: 198 CHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLFIG 257 C IGGN ATNAGG R +R+G++ +LGLEV L DGT+L + + K+ TG DLKQLFIG Sbjct: 142 CQIGGNAATNAGGNRVIRFGTMRDLILGLEVALPDGTMLSMMNRVTKNTTGIDLKQLFIG 201 Query: 258 SEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDAVC 317 SEGTLG+IT + + PKP AVN A F + + + L LS+FE M Sbjct: 202 SEGTLGVITRIVLKLEPKPSAVNTALCAVASFDDATRLLKYLRARLAN-LSSFELMWQDF 260 Query: 318 MQLVGRHLHLASPVQES-PFYVLIETSGSNAGHDAEKLGHFLEHALGSGLVTDGTMATDQ 376 M HL +P ++ P YVLIET G + D L H LE L G+V D +A Sbjct: 261 MSAAMDIAHLKAPFGDTYPVYVLIETLGESDDDDRRALEHSLERMLDDGIVQDVIIAQSI 320 Query: 377 RKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIVTDLRARLGPHAKHV--VGYGH 434 K LWA RE + E LS+ +D+ +P++R+ V D RA L + +GH Sbjct: 321 EHAKQLWAYRETVGELLSKLKPHAAFDIGIPMDRMNGFVEDARAALNERFSQQAHLFFGH 380 Query: 435 LGDGNLHLNVTAEAFSPSLLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGA 494 LGDGNLHL A + LL +E +Y QG +SAEHG+G K+ L YS+ Sbjct: 381 LGDGNLHLLSGPYADAADLL-KVEELIYAAVNDVQGCISAEHGIGVIKQPFLHYSRSAPE 439 Query: 495 LQLMQQLKALLDPKGILN 512 L LM +LKALLDP GILN Sbjct: 440 LDLMGKLKALLDPAGILN 457 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: 610 Number of extensions: 22 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: 463 Length adjustment: 34 Effective length of query: 487 Effective length of database: 429 Effective search space: 208923 Effective search space used: 208923 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