Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 6938321 Sama_2440 iron-sulfur cluster-binding protein (RefSeq)
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__SB2B:6938321 Length = 935 Score = 1457 bits (3771), Expect = 0.0 Identities = 703/934 (75%), Positives = 807/934 (86%) Query: 1 MSINYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTV 60 MS++YK VI L+++LG + V+DDPVRRFAWSTDASYFRIVPEVVVHA++L++V+ TL + Sbjct: 1 MSVDYKAVIEALKSRLGPQAVSDDPVRRFAWSTDASYFRIVPEVVVHADSLDEVQQTLAI 60 Query: 61 ARKHNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANA 120 AR+H APVTFRAAGTSLSGQAIG GILL+LGHDGFR+++VSSD +++LGAAVIG+DANA Sbjct: 61 AREHGAPVTFRAAGTSLSGQAIGPGILLMLGHDGFRQLKVSSDGTKVSLGAAVIGADANA 120 Query: 121 VLAPLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTG 180 L L++KIGPDPAT+ASA IGGIV NNASGMCCGTAQNSYQTI S +++ ADGT LDTG Sbjct: 121 ALKALDKKIGPDPATLASAMIGGIVNNNASGMCCGTAQNSYQTIDSLRMVLADGTVLDTG 180 Query: 181 CEKSKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPF 240 E S+ F ++HG LL DLS L+ + + N LA RIRKKY+IKNTTGY +N+L+DF+ PF Sbjct: 181 SEASRQAFEQSHGALLNDLSNLAAMVKANHGLAARIRKKYAIKNTTGYSLNALVDFSCPF 240 Query: 241 DIINHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAE 300 DIINHLMVG EGTL F+ +VTYHTV+EA+FKASAMAVF +ME+AA AIP + G+SV+AAE Sbjct: 241 DIINHLMVGSEGTLGFVEQVTYHTVDEARFKASAMAVFFSMEEAASAIPFLIGKSVAAAE 300 Query: 301 LLDWPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIR 360 LLDW SI+AVTGK GMPDWLS LP +AILLIESRA DA TL+ YT++V K+A R Sbjct: 301 LLDWASIRAVTGKKGMPDWLSSLPEGAAILLIESRAADADTLQAYTEEVIGKIAHIPTER 360 Query: 361 PMEFSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHK 420 P+ FST+PAVY KYWAMR GLFPI+GGERPKG+SVIIEDVAFE++HLAAAA D+T LFH+ Sbjct: 361 PIVFSTDPAVYSKYWAMRSGLFPIIGGERPKGSSVIIEDVAFEVQHLAAAAKDLTALFHE 420 Query: 421 HGYPEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTG 480 HGYPEG IYGHALAGNFHFIITP F +Q DIDRFH FM +A+MVINKY+GSMKAEHGTG Sbjct: 421 HGYPEGVIYGHALAGNFHFIITPTFASQGDIDRFHGFMQAVAEMVINKYDGSMKAEHGTG 480 Query: 481 RAVAPFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVD 540 RAVAPFVE EWG +AYTLMK+IK +FDP G+LNPGVILNDD+ +HVKNIKPCPVVDD VD Sbjct: 481 RAVAPFVEMEWGSEAYTLMKSIKSLFDPSGLLNPGVILNDDATVHVKNIKPCPVVDDLVD 540 Query: 541 KCIECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAA 600 KCIECGFCEKTCPTSALN +PRQRIATLREI RLE SGD+ AA++MR AKYDV+DTCAA Sbjct: 541 KCIECGFCEKTCPTSALNLTPRQRIATLREISRLEASGDEEAASRMRDAAKYDVVDTCAA 600 Query: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHK 660 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFD LGVIHK Sbjct: 601 CQLCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDTLGVIHK 660 Query: 661 ITGDGITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGP 720 +TGD +T+ALMK GR++SKEVPYW+P FPKGG LPK P K GQET+VYFPACGGRTFGP Sbjct: 661 LTGDTVTSALMKVGRMVSKEVPYWDPSFPKGGALPKLPPHKVGQETLVYFPACGGRTFGP 720 Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780 TP D D R LPEVVV +LERAGYNV+ PE TR LCCGQMWESKGDFKNAD KR+ELI+ L Sbjct: 721 TPLDKDKRPLPEVVVQVLERAGYNVVIPEHTRSLCCGQMWESKGDFKNADGKRRELIEAL 780 Query: 781 SKMSNGGKIPVLVDALSCTYRTLTGNPQVQITDLVEFMHDKLLDKLSINKKVNVALHLGC 840 S GK+ V+VDALSCT RTL G+P V+I DLVEF+HD +L +LSI +K V LHLGC Sbjct: 781 KAKSENGKLKVVVDALSCTKRTLGGDPDVEILDLVEFLHDDVLSRLSIRQKPLVTLHLGC 840 Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900 SAR +K+E KMQAIA+ C+ +V KPAGIECCGYAGEKGLYKPEINASALRNIKKL+P Sbjct: 841 SARHLKVEAKMQAIADTCAKEVHKPAGIECCGYAGEKGLYKPEINASALRNIKKLLPAAA 900 Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 EGYYANRMCEVGL++HSGISYRHL YLLEECSR Sbjct: 901 TEGYYANRMCEVGLSKHSGISYRHLVYLLEECSR 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: 2276 Number of extensions: 78 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: 935 Length adjustment: 43 Effective length of query: 891 Effective length of database: 892 Effective search space: 794772 Effective search space used: 794772 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 Apr 09 2024. 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