Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 7025755 Shewana3_2905 FAD linked oxidase domain-containing protein (RefSeq)
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__ANA3:7025755 Length = 934 Score = 1649 bits (4269), Expect = 0.0 Identities = 807/934 (86%), Positives = 864/934 (92%) Query: 1 MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60 MSINY V +L QLG+ V++DPVRRFAWSTDASYFRIVPE+VVHA+TLEQ K TL + Sbjct: 1 MSINYDAVYKELIQQLGESAVSNDPVRRFAWSTDASYFRIVPEIVVHADTLEQAKQTLAI 60 Query: 61 ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120 AR H PVTFRAAGTSLSGQAIGEGILLILGHDGFR I++S D+ +ITLGAAVIG+DANA Sbjct: 61 ARAHKVPVTFRAAGTSLSGQAIGEGILLILGHDGFRTIDISPDSNKITLGAAVIGADANA 120 Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180 L PLN+KIGPDPAT+ASA +GGIV+NNASGMCCGTAQNSYQTIASAKLLFADGTEL+TG Sbjct: 121 ALKPLNKKIGPDPATLASAMVGGIVSNNASGMCCGTAQNSYQTIASAKLLFADGTELNTG 180 Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240 C+KSKA F ++HG LL L+ L+ LTR N LA+RIRKKYSIKNTTGY IN+L+DF DPF Sbjct: 181 CDKSKAAFTQSHGDLLDSLASLAKLTRSNEVLAQRIRKKYSIKNTTGYSINALVDFEDPF 240 Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300 D+INHL+VG EGTLAF+ EVTYHTV+EAKFKASAMAVF NM DAA AIP I G+SV+AAE Sbjct: 241 DLINHLIVGAEGTLAFVEEVTYHTVDEAKFKASAMAVFFNMVDAASAIPPIIGDSVAAAE 300 Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360 LLDW SIKAVTGK GMPDWL+ELP +AILLIESRA+DAQTLE YTQDV AKLA R Sbjct: 301 LLDWASIKAVTGKKGMPDWLNELPEGAAILLIESRANDAQTLESYTQDVIAKLAHIKTER 360 Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420 P+ FS++ VY KYWAMR GLFPI+GGERPKG+SVIIEDVAF +EHLAAAA D+TELFHK Sbjct: 361 PISFSSDANVYSKYWAMRSGLFPIIGGERPKGSSVIIEDVAFNVEHLAAAAADLTELFHK 420 Query: 421 HGYPEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTG 480 HGYPEG IYGHALAGNFHFIITP F +QADI+RF FM D+A+MVI+KY+GSMKAEHGTG Sbjct: 421 HGYPEGVIYGHALAGNFHFIITPTFASQADIERFQGFMQDVAEMVIHKYDGSMKAEHGTG 480 Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540 RAVAPFVE EWG DAYTLMK IK +FDP+G+LNPGVILNDDS +HVKNIKPCPVVDDFVD Sbjct: 481 RAVAPFVEMEWGADAYTLMKRIKHIFDPEGLLNPGVILNDDSTVHVKNIKPCPVVDDFVD 540 Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAA 600 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAA KMRADAKYDVIDTCAA Sbjct: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAEKMRADAKYDVIDTCAA 600 Query: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK Sbjct: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660 Query: 661 ITGDGITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720 ITGDGITNALMKTGRL+SKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP Sbjct: 661 ITGDGITNALMKTGRLLSKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720 Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDV+ Sbjct: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVV 780 Query: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC Sbjct: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840 Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900 SARKMKLEPKMQAIA+ACS+QV KPAGI+CCGYAGEKGLYKPEINASALRNIKKLIPVE+ Sbjct: 841 SARKMKLEPKMQAIADACSSQVHKPAGIDCCGYAGEKGLYKPEINASALRNIKKLIPVEI 900 Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR Sbjct: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 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: 2460 Number of extensions: 82 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: 934 Length adjustment: 43 Effective length of query: 891 Effective length of database: 891 Effective search space: 793881 Effective search space used: 793881 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