Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate GFF922 Psest_0951 FAD/FMN-containing dehydrogenases
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__psRCH2:GFF922 Length = 950 Score = 773 bits (1996), Expect = 0.0 Identities = 410/919 (44%), Positives = 571/919 (62%), Gaps = 14/919 (1%) Query: 23 DDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAI 82 DDP+ A+ TDAS++R++P++VV E+ +V L +A N PVTFRAAGTSLSGQAI Sbjct: 31 DDPLSTLAFGTDASFYRLIPKLVVRVESEAEVIALLKLAHAENVPVTFRAAGTSLSGQAI 90 Query: 83 GEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIG 142 + +L++LG D + E+ + +QI L VIG++ANAVLAP RKIGPDPA+I +AKIG Sbjct: 91 SDSVLIVLG-DNWNGREIRNGGEQIRLQPGVIGANANAVLAPFQRKIGPDPASINAAKIG 149 Query: 143 GIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSEL 202 GIVANN+SGMCCGTAQN+Y+T+A +++ ADGT +D+ S F ++H LL+ L+EL Sbjct: 150 GIVANNSSGMCCGTAQNTYKTLAGLRVVLADGTVVDSEDAASVDAFRQSHAALLEQLAEL 209 Query: 203 SHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTY 262 TR NS LA +IR KY +KNTTG+ +N+L+D+ +P DI+NHLMVG EGTL FI+ VTY Sbjct: 210 GRETRANSELAAKIRHKYRLKNTTGFSLNALVDYDEPLDILNHLMVGSEGTLGFISAVTY 269 Query: 263 HTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSE 322 TV + KASA+ VF ++E A+P++ + VSA ELLD S+++V K GMP+W+ E Sbjct: 270 DTVPDHPHKASALVVFPDVETCCLAVPVLKQQPVSAVELLDRRSLRSVEHKVGMPEWVKE 329 Query: 323 LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLF 382 L + LLIESRA L + +A F + ++FS +P +Y++ W +RK F Sbjct: 330 LSPTACALLIESRAASQSLLHEQINLIMTSIAHFPVEKQVDFSEDPVIYNQLWKIRKDTF 389 Query: 383 PIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIIT 442 P VG R GT+VIIEDV F +E LA + + EL KH Y E ++GHAL GN HF+ T Sbjct: 390 PAVGAVRQTGTTVIIEDVTFPVERLAEGVNRLIELLDKHRYDEAILFGHALEGNLHFVFT 449 Query: 443 PAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNI 502 F A + R+ AFM ++A +V ++ G++KAEHGTGR +APFVE EWG +AY LM I Sbjct: 450 QGFDDPAQVARYEAFMGEVAQLVAVEFGGALKAEHGTGRNMAPFVELEWGSEAYALMWKI 509 Query: 503 KQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPR 562 K++ DP GILNP V+L++D +IH+KN+KP P D+ VDKCIECGFCE CP++ L +PR Sbjct: 510 KRLLDPTGILNPDVVLSEDPDIHLKNLKPMPAADEIVDKCIECGFCEPVCPSNGLTLTPR 569 Query: 563 QRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLR 622 QRI R+I+ +++G ++ Y I+TCAA LC CPV + G L+RKLR Sbjct: 570 QRIVIWRDIQARKRAG--VDTTEIERLYHYHGIETCAATGLCAQRCPVGINTGDLIRKLR 627 Query: 623 TPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISK-EV 681 S T ++ A HF Q H I G L T SK V Sbjct: 628 GREASKT--GAANWLADHFATAVQGTRFMLHAANGAHIILGTKRLAKLSATMTNASKGRV 685 Query: 682 PYWNPDFPKGGK---LPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLL 738 P W P P+ + LPKP+ A+ + VVY AC R P +D + L + +LL Sbjct: 686 PQWTPATPQPLQRLHLPKPT-AQDERPRVVYLAACVSRAMAPAARDQEQEPLLDKTRSLL 744 Query: 739 ERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSC 798 E+AGY VI PE+ DLCCGQ + SKG + + KRQE++D L K S GG P+ D C Sbjct: 745 EKAGYQVIFPEQLNDLCCGQPFASKGYAEQGERKRQEMLDALLKASRGGLDPIYCDTSPC 804 Query: 799 TYRTLTG--NPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGCSARKMKLEPKMQAIA 855 T R + G + ++ + D V F+ LLDKL + ++ +A+H+ CS + + + IA Sbjct: 805 TLRLVQGLTDQRLDLYDPVRFIRTYLLDKLDFVPQEKAIAVHVTCSTQHLGEAQALIDIA 864 Query: 856 NACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLT 915 C+ +V+ P GI CCG+AG+KG PE+N ALR++K + + EG +R CE+GL+ Sbjct: 865 RRCAKEVVVPEGIHCCGFAGDKGFTTPELNCHALRSLKDAVQI-CDEGISTSRTCEIGLS 923 Query: 916 QHSGISYRHLAYLLEECSR 934 +H I Y L YL++ +R Sbjct: 924 RHGEIDYHGLVYLVDRVTR 942 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: 2074 Number of extensions: 87 Number of successful extensions: 7 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: 950 Length adjustment: 44 Effective length of query: 890 Effective length of database: 906 Effective search space: 806340 Effective search space used: 806340 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