Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate AZOBR_RS25120 AZOBR_RS25120 4Fe-4S ferredoxin
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__azobra:AZOBR_RS25120 Length = 962 Score = 845 bits (2184), Expect = 0.0 Identities = 439/934 (47%), Positives = 591/934 (63%), Gaps = 13/934 (1%) Query: 12 LRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFR 71 LR + D + DP+R A+ TD S++R++P++V E +V L + R+ PVTFR Sbjct: 13 LREFMPDERLVTDPLRTLAYGTDGSFYRLIPKIVAIVEAEGEVVRLLNLCRELKTPVTFR 72 Query: 72 AAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGP 131 AAGTSLSGQA+ + +L++LG D +R + A +TL VIG++AN LAP RKIGP Sbjct: 73 AAGTSLSGQAVTDSVLVLLG-DSWRGCTIPPGAATVTLQPGVIGAEANRKLAPFGRKIGP 131 Query: 132 DPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKT 191 DPA+IA+AKIGGI ANNASGMCCGTAQNSY+T+AS +L+ ADGT LDTG S+A FA + Sbjct: 132 DPASIATAKIGGIAANNASGMCCGTAQNSYRTLASMRLVLADGTLLDTGDAASRAAFAVS 191 Query: 192 HGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGME 251 HG LL LS+L+ TR + LAERIR K+ IKNTTGY +N+L+DF +P +I+ HLM+G E Sbjct: 192 HGALLSGLSDLAARTRADDKLAERIRNKFRIKNTTGYSLNALVDFEEPVEILQHLMIGSE 251 Query: 252 GTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVT 311 GTL F++E+TY+TV E KA+A+ ++ ++ +A RA+ L+ VSA EL+D S+++V Sbjct: 252 GTLGFLSEITYNTVPEHAHKANALLMYPDIGEACRAVALMKPTPVSAVELMDRASLRSVE 311 Query: 312 GKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVY 371 GKPGMPD++ L ++ LL+E R +DA L+ V+A +A + P F+T+ + Sbjct: 312 GKPGMPDFIGGLGPDASALLVEIRGEDAAALDANIAAVSAVIAQTQTLFPPTFTTDAKLG 371 Query: 372 DKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGH 431 + YW +RKGLFP VG R GT+VIIEDVA+ L+ LA A ++ +F K GY E I+GH Sbjct: 372 ESYWKIRKGLFPAVGAMRKVGTTVIIEDVAYPLDRLAEATVELQAMFLKFGYTEAIIFGH 431 Query: 432 ALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEW 491 AL GN HF+ T AF T ++DR+ FMD + D V+ KY+GS+KAEHGTGR +APFVE EW Sbjct: 432 ALEGNLHFVFTQAFDTDEEVDRYRRFMDAVCDQVVRKYDGSLKAEHGTGRNMAPFVEMEW 491 Query: 492 GQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKT 551 G AY LMK IK + DPQG+LNPGVILNDD H+KN+K P VD CIECGFCE T Sbjct: 492 GPQAYGLMKEIKALLDPQGLLNPGVILNDDPEAHLKNLKAMPAAHPLVDTCIECGFCEPT 551 Query: 552 CPTSALNFSPRQRIATLREIERLEQSG-DKAAAAKMRADAKYDVIDTCAACQLCTIACPV 610 CP+ + SPRQRI REI RLE +G D A + Y IDTCAAC LC+ ACPV Sbjct: 552 CPSHKMTLSPRQRIVGWREISRLEATGADAARLGALHEAYDYQGIDTCAACGLCSTACPV 611 Query: 611 DNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNAL 670 G L++ +R T Q + A+H V TG + + + GD N L Sbjct: 612 GIETGLLIKAIRGDRRGTMAQGFGTYVAEHTAGALSVARTGLKLADLAKRTLGDDTANGL 671 Query: 671 M-KTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQE-------TVVYFPACGGRTFGPTP 722 K + + +P+ P AKA + TVVY P+C R+ GP Sbjct: 672 FEKLRNVTGQRLPHLPRALPTPTNFTPLPQAKASADAPTANTPTVVYVPSCTSRSMGPAA 731 Query: 723 KDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSK 782 DP+ LP V L ++AGY V PE+ LCCG ESKG ADAK +E++ + Sbjct: 732 NDPEKTPLPVKVEALFQKAGYRVAYPEQLASLCCGMPLESKGLAAQADAKAEEMVRAIWA 791 Query: 783 MSNGGKIPVLVDALSCTYRTL--TGNPQVQITDLVEFMHDKLLDKLSINKKVN-VALHLG 839 S G PV++D C++R + +Q+ DLVEF+HD LLD+L+ K+ V LHL Sbjct: 792 ASADGTAPVVLDTSPCSFRLKKHLKDAGLQVLDLVEFIHDHLLDRLNFTKQTEPVVLHLT 851 Query: 840 CSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVE 899 CS R+M L+ KM+A+A AC+ QV+ P + CCG+AG+KG PE+NA ALR++ K IP Sbjct: 852 CSTRRMGLDAKMKAVAAACATQVVVPEDVGCCGFAGDKGFTTPELNAHALRHLSKDIPAG 911 Query: 900 VKEGYYANRMCEVGLTQHSGISYRHLAYLLEECS 933 K GY +R CE+GL+ HSG+ YR + YL++ CS Sbjct: 912 AKAGYSNSRTCEIGLSDHSGLPYRSIVYLVDACS 945 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: 2207 Number of extensions: 81 Number of successful extensions: 8 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: 962 Length adjustment: 44 Effective length of query: 890 Effective length of database: 918 Effective search space: 817020 Effective search space used: 817020 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