Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 200692 SO1521 iron-sulfur cluster-binding protein (NCBI ptt file)
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__MR1:200692 Length = 914 Score = 1842 bits (4772), Expect = 0.0 Identities = 913/914 (99%), Positives = 914/914 (100%) Query: 21 VTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQ 80 +TDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQ Sbjct: 1 MTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQ 60 Query: 81 AIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAK 140 AIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAK Sbjct: 61 AIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAK 120 Query: 141 IGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLS 200 IGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLS Sbjct: 121 IGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLS 180 Query: 201 ELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEV 260 ELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEV Sbjct: 181 ELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEV 240 Query: 261 TYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWL 320 TYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWL Sbjct: 241 TYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWL 300 Query: 321 SELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKG 380 SELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKG Sbjct: 301 SELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKG 360 Query: 381 LFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFI 440 LFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFI Sbjct: 361 LFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFI 420 Query: 441 ITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMK 500 ITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMK Sbjct: 421 ITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMK 480 Query: 501 NIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFS 560 NIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFS Sbjct: 481 NIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFS 540 Query: 561 PRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRK 620 PRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRK Sbjct: 541 PRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRK 600 Query: 621 LRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISKE 680 LRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISKE Sbjct: 601 LRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISKE 660 Query: 681 VPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLER 740 VPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLER Sbjct: 661 VPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLER 720 Query: 741 AGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTY 800 AGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTY Sbjct: 721 AGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTY 780 Query: 801 RTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGCSARKMKLEPKMQAIANACSA 860 RTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGCSARKMKLEPKMQAIANACSA Sbjct: 781 RTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGCSARKMKLEPKMQAIANACSA 840 Query: 861 QVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLTQHSGI 920 QVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLTQHSGI Sbjct: 841 QVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLTQHSGI 900 Query: 921 SYRHLAYLLEECSR 934 SYRHLAYLLEECSR Sbjct: 901 SYRHLAYLLEECSR 914 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: 2614 Number of extensions: 90 Number of successful extensions: 3 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: 914 Length adjustment: 43 Effective length of query: 891 Effective length of database: 871 Effective search space: 776061 Effective search space used: 776061 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