Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate AO356_07570 AO356_07570 4Fe-4S ferredoxin
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07570 Length = 955 Score = 770 bits (1989), Expect = 0.0 Identities = 408/931 (43%), Positives = 573/931 (61%), Gaps = 11/931 (1%) Query: 9 INDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPV 68 + D++ + + DDP+ A+ TDAS++R++P++VV E+ ++V L +A++ PV Sbjct: 8 LRDVQQLIPQKRRFDDPLSTLAFGTDASFYRLIPKLVVRVESEDEVIALLKLAQRDQVPV 67 Query: 69 TFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRK 128 TFRAAGTSLSGQAI + +L++LG D + E+ QI L VIG+ ANA LAP RK Sbjct: 68 TFRAAGTSLSGQAISDSVLIVLG-DNWNGREIREQGTQIRLQPGVIGAQANAWLAPFGRK 126 Query: 129 IGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEF 188 IGPDPA+I + KIGGIVANNASGMCCGTAQN+Y T+A +L+ ADGT LDT + S A F Sbjct: 127 IGPDPASINACKIGGIVANNASGMCCGTAQNTYHTLAGIRLVLADGTRLDTEDDNSVAAF 186 Query: 189 AKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMV 248 +HG+LL+ L+ L TR N+ LA RIR KY +KNTTG +N+L+DF +P DI++HL+V Sbjct: 187 RTSHGELLERLATLGRETRANTELAARIRHKYRLKNTTGLSLNALVDFDEPVDILSHLLV 246 Query: 249 GMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIK 308 G EGTL FI+ VTY+TV + KASA+ VF ++E A+ ++ + VSA ELLD S++ Sbjct: 247 GSEGTLGFISAVTYNTVIDHPNKASALIVFPDVETCCNAVTVLKSQPVSAVELLDRRSLR 306 Query: 309 AVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNP 368 +V KPGMPD++ L + LLIESRA + L+ + LAGF + ++F+ +P Sbjct: 307 SVQDKPGMPDFVQHLSINACALLIESRAASSSLLQEQLARIMTSLAGFPVEKQVDFTEDP 366 Query: 369 AVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCI 428 + WA+RK FP VG R GT+VIIEDV F +E LA + + ELF KH Y E + Sbjct: 367 RENARLWAIRKDTFPAVGAVRKTGTTVIIEDVTFPVEQLALGVNRLIELFDKHHYDEAIL 426 Query: 429 YGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVE 488 +GHAL GN HF+ T F + ++ R+ AFMDD+A +V ++ GS+KAEHGTGR +APFVE Sbjct: 427 FGHALEGNLHFVFTQGFNSAEEVARYQAFMDDVAHLVAVEFGGSLKAEHGTGRNMAPFVE 486 Query: 489 KEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFC 548 EWG DAY LM +K++ DP GILNP V+L++D IH+K++KP P D+ VDKCIECGFC Sbjct: 487 LEWGSDAYQLMWQLKRLLDPNGILNPDVVLSEDPQIHLKHLKPLPAADEIVDKCIECGFC 546 Query: 549 EKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIAC 608 E CP+ L SPRQRI R+I+ +++G ++ +Y IDTCAA LC C Sbjct: 547 EPVCPSKDLTLSPRQRIVIWRDIQAKKRAG--TDTTELERAYQYQGIDTCAATGLCAQRC 604 Query: 609 PVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG-DGIT 667 PV + G+LV+KLR+ T+ K ++ +F Q V + G + Sbjct: 605 PVGINTGELVKKLRSR--DATKTKTANWIEGNFATTLQGARFALHVANGARMLLGAPRLA 662 Query: 668 NALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQE-TVVYFPACGGRTFGPTPKDPD 726 RL +VP W P+ K + SP + + VVY AC R GPT D + Sbjct: 663 KLSASLTRLSKGQVPQWTNAMPQPEKAIRFSPTVSDERPRVVYLAACVSRVMGPTAADKE 722 Query: 727 NRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNG 786 +L + +LLE+AGY V+ P+ LCCGQ + SKG + A+ KRQELI L S G Sbjct: 723 QMSLYDKTRSLLEKAGYQVVFPDNVDSLCCGQPFASKGYTEQAEHKRQELIGALLHASRG 782 Query: 787 GKIPVLVDALSCTYRTL--TGNPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGCSAR 843 G P+ D CT R + G+ ++ + D V F+ L+++L I ++ +A+H+ CS + Sbjct: 783 GLDPIYCDTSPCTLRLVQDLGDVRLDLYDPVRFIRTHLMERLDFIPQEAPIAVHVTCSTQ 842 Query: 844 KMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEG 903 + + +A CS V+ P GI CCG+AG+KG PE+NA +LR +K + EG Sbjct: 843 HLGESQALIDLARKCSKNVVIPEGIHCCGFAGDKGFTTPELNAHSLRTLKDAVQY-CTEG 901 Query: 904 YYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 +R CE+GLT+HS I Y L YL++ +R Sbjct: 902 ISTSRTCEIGLTRHSEIDYHGLVYLVDRVTR 932 Lambda K H 0.319 0.135 0.402 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: 2033 Number of extensions: 71 Number of successful extensions: 9 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: 934 Length of database: 955 Length adjustment: 44 Effective length of query: 890 Effective length of database: 911 Effective search space: 810790 Effective search space used: 810790 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 (21.7 bits) S2: 57 (26.6 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