Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Pf1N1B4_4424 D-2-hydroxyglutarate dehydrogenase
Query= BRENDA::Q8N465 (521 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4424 Length = 474 Score = 284 bits (726), Expect = 6e-81 Identities = 174/429 (40%), Positives = 240/429 (55%), Gaps = 17/429 (3%) Query: 104 LRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFD--EIILSTARMNRVLSFHS 161 + P ++EEV+ ++R C + V QGGNTG++GG+ P ++L RMNRV + + Sbjct: 43 VHPASTEEVAAVVRACVACDTPVVVQGGNTGLMGGATPDASGRAVLLLLDRMNRVRAVDT 102 Query: 162 VSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHG 221 + L +AGC+L+ + + + PL LGA+GSC IGGN+ TNAGG LRYG+ Sbjct: 103 DNDTLTVEAGCILQTIQDVARDAGRLFPLSLGAEGSCTIGGNLGTNAGGTAVLRYGNTRE 162 Query: 222 TVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNV 281 +LGLEVV A G + + L LRKDNTGYDL+ LFIGSEGTLGIIT ++ P P+A Sbjct: 163 LILGLEVVTAQGEIWNGLRGLRKDNTGYDLRDLFIGSEGTLGIITAATLKLFPLPKAQAT 222 Query: 282 AFLGCPGFAEVLQTFSTCKGMLGEILSAFEFMDAVCMQLVGRHLHLASPV----QESPFY 337 A L A+ + S + G L+AFE ++A C+ L+ R P P++ Sbjct: 223 ALLAFDSLAQAVTFLSHARAGFGASLTAFELLNAECLALL-REQFPEGPQPFLGARQPWF 281 Query: 338 VLIETSGSNA-GHDAEKLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRD 396 L+E S +++ H E L A L+ D +A + + LW LRE ++EA R Sbjct: 282 ALLELSDNHSESHAREAFEQVLGEAFEQRLLADALIAESLAQSQALWLLRENMSEAQKRA 341 Query: 397 GYVYKYDLSLPVERLYDIVTDLRARLGPHAKHVVGY--GHLGDGNLHLNV------TAEA 448 G K+D+S+P+ ++ V D A L H V Y GHLGDGNLH NV T EA Sbjct: 342 GRNMKHDISVPISQVVAFVADTDALLQCHFPGVRHYTFGHLGDGNLHYNVAHPQDSTVEA 401 Query: 449 FSPSLLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPK 508 AAL V++ GS+SAEHG+G KRD+LG K P L LM+++K LDPK Sbjct: 402 HMVH-YAALSQLVHDSAHAHGGSISAEHGIGQHKRDMLGRYKSPVELDLMRRIKQALDPK 460 Query: 509 GILNPYKTL 517 +LNP K L Sbjct: 461 NLLNPGKVL 469 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: 620 Number of extensions: 28 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: 474 Length adjustment: 34 Effective length of query: 487 Effective length of database: 440 Effective search space: 214280 Effective search space used: 214280 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