Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate RR42_RS07415 RR42_RS07415 2-hydroxyacid dehydrogenase
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__Cup4G11:RR42_RS07415 Length = 470 Score = 301 bits (770), Expect = 4e-86 Identities = 185/476 (38%), Positives = 263/476 (55%), Gaps = 30/476 (6%) Query: 65 QDLAAFERIV----PGGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCH 120 QDLA R++ P V T+P+ + DW RG ++ ++RPR+ +EV+ L C Sbjct: 2 QDLAFLPRLIEALGPDVVATEPDQVAPWLADWRGLYRGNAQAVVRPRSVDEVARCLALCQ 61 Query: 121 ERNLAVNPQGGNTGMVGGSVPVFD--EIILSTARMNRVLSFHSVSGILVCQAGCVLEELS 178 + + V P+GGNTG+ GG+ P ++LS RMN + S +++ L+ +AGC+L L Sbjct: 62 QAAVPVVPRGGNTGLCGGAAPDSSPANVVLSMDRMNAIRSIDTIANTLIAEAGCILGNLR 121 Query: 179 RYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDC 238 R +E ++PL L A+ SC IGGN+ATNAGG+ +RYG VLG+E VL +G + Sbjct: 122 RAAQEAHRLLPLSLAAEDSCQIGGNLATNAGGVNVVRYGMTRELVLGVEAVLPNGEIFHG 181 Query: 239 LTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFST 298 L +LRKDNTGYDLKQL IGSEGTLG+IT ++ P+ A +V + L+ F Sbjct: 182 LRALRKDNTGYDLKQLLIGSEGTLGVITAAALRLFPRTDARSVVLAAVASPLQALELFEL 241 Query: 299 CKGMLGEILSAFEFMDAVCMQLVGRHLHLASPVQES-----PFYVLIETSGSNAGHDAEK 353 G L AFEF C+ LV +H A VQE P YVL+E + + D Sbjct: 242 LFAQCGARLQAFEFFTGDCVDLVLKH---AEGVQEPFSQRYPAYVLVELADTT---DEAA 295 Query: 354 LGHFLEHALGSG----LVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVE 409 L LE +G L D ++ +++ LW LRE I+EA DG K+D+SLP+E Sbjct: 296 LNVLLERVIGEALERELCLDAAVSASLSQLQSLWKLREEISEAQRADGPHLKHDVSLPIE 355 Query: 410 RLYDIVTDLRARL---GPHAKHVVGYGHLGDGNLHLNVTAEA-----FSPSLLAALEPHV 461 ++ + + ARL P + + +GH GDGNLH N++ A ++ AL V Sbjct: 356 QIPAFMVSMEARLKAISPSIRPFI-FGHFGDGNLHYNLSRPAGAQRDWTAQHGKALTAEV 414 Query: 462 YEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517 + A GS+SAEHG+G KRD K P L++M+ +K LLDP GI+NP K L Sbjct: 415 LDEVARYGGSISAEHGIGQLKRDDFLRLKDPLELRMMRGIKQLLDPAGIMNPGKLL 470 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: 640 Number of extensions: 29 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: 470 Length adjustment: 34 Effective length of query: 487 Effective length of database: 436 Effective search space: 212332 Effective search space used: 212332 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