Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate HSERO_RS16560 HSERO_RS16560 2-hydroxyacid dehydrogenase
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__HerbieS:HSERO_RS16560 Length = 468 Score = 292 bits (747), Expect = 2e-83 Identities = 178/456 (39%), Positives = 253/456 (55%), Gaps = 20/456 (4%) Query: 78 VVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVG 137 V+TD D G + +LRP S EV+ ++R C + + + PQGGNTG+V Sbjct: 17 VLTDAHDTAGYLTDQRGRYTGRALAVLRPADSAEVAAVVRLCAQFAVPLVPQGGNTGLVL 76 Query: 138 GSVP--VFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAK 195 GSVP + ++LS R+NR+ + +++ + ++GCVL+ L + PL L A+ Sbjct: 77 GSVPDQQGNAVVLSLRRLNRIRAVDALNNTITVESGCVLQHLQEQAAAAGRLFPLSLAAE 136 Query: 196 GSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLF 255 GSC IGGN++TNAGG LRYG+ LGLEVV A G ++ L LRKDNTGYDL+ LF Sbjct: 137 GSCTIGGNLSTNAGGTGVLRYGNTRELCLGLEVVTAQGEIMSSLKGLRKDNTGYDLRDLF 196 Query: 256 IGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDA 315 IG+EGTLG+IT + P+PRA A P A+ LQ + G L+ FE M Sbjct: 197 IGAEGTLGVITAAVMKLFPQPRAQVTALAALPHPAQALQLLQLAQAHCGPALTGFELMSD 256 Query: 316 VCMQLVGRHLHLASPVQESPF------YVLIETSGSNAGHDAEKLGH-FLEHALGSGLVT 368 C+QLV +H P Q PF YVL+E S S + A L + AL GLV Sbjct: 257 FCLQLVRKHF----PEQRLPFDRPHPQYVLLELSDSESEEHARALFEGLIGTALEQGLVD 312 Query: 369 DGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIV--TDLRARLGPHA 426 D +A + + LW LRE I+ A + +G K+D+S+P+ R+ + + TD+ + Sbjct: 313 DAVIAASLAQSRALWRLRESISSAQAHEGKNIKHDISVPISRIAEFIAATDVLVQQAAPG 372 Query: 427 KHVVGYGHLGDGNLHLNVT-----AEAFSPSLLAALEPHVYEWTAGQQGSVSAEHGVGFR 481 +V +GHLGDGNLH NV+ A+ + AA+ V++ GS+SAEHG+G Sbjct: 373 CRMVTFGHLGDGNLHYNVSPPEGVADRDFIARQAAINRVVHDSVDRFGGSISAEHGLGAL 432 Query: 482 KRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517 KR+ + K P LQLM+ +K LDP+ ++NP K L Sbjct: 433 KREEITRYKSPVELQLMRAIKLALDPQQLMNPGKVL 468 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: 666 Number of extensions: 41 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: 468 Length adjustment: 34 Effective length of query: 487 Effective length of database: 434 Effective search space: 211358 Effective search space used: 211358 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