Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate GFF4151 HP15_4091 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__Marino:GFF4151 Length = 938 Score = 765 bits (1975), Expect = 0.0 Identities = 408/934 (43%), Positives = 565/934 (60%), Gaps = 12/934 (1%) Query: 7 EVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNA 66 EV+ ++R ++ + V +DP+ A+ TDAS++R++P+VVV + +V L +AR+H Sbjct: 6 EVLANIRQRIPENRVFNDPMSTLAFGTDASFYRLIPKVVVRVQDEAEVVDLLAIARRHKV 65 Query: 67 PVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLN 126 PVTFRAAGTSLSGQAI + IL++LG D + ++ + +QI L VIG+ ANA LAP Sbjct: 66 PVTFRAAGTSLSGQAISDSILIVLG-DQWNGHDIREEGRQIRLQPGVIGAQANAWLAPKG 124 Query: 127 RKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKA 186 KIGPDPA+I + KIGGIVANNASGMCCGTAQNSY T+A +L+ ADG LDT S + Sbjct: 125 FKIGPDPASINACKIGGIVANNASGMCCGTAQNSYHTLAGMRLVLADGAVLDTEDPASVS 184 Query: 187 EFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHL 246 F +HG LL L +L+ TR N LAERIR KY +KNTTG +N+L+DFT P DI+ HL Sbjct: 185 AFRDSHGDLLAALKKLAINTRENPELAERIRHKYRLKNTTGLSLNALVDFTCPLDILTHL 244 Query: 247 MVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPS 306 MVG EGTL F++ VTY+TV E KA+A+ VF + E RA + + V+A ELLD S Sbjct: 245 MVGSEGTLGFVSAVTYNTVPEYPDKATALLVFRDAESCCRAASALRSQPVAAVELLDRRS 304 Query: 307 IKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFST 366 +++V KPG+PDW+ +L + LL+E+RA ++ L+ + LA F + ++F+ Sbjct: 305 LRSVQYKPGLPDWIHDLSESACALLVETRASSSEILDEQLTRIRQALAEFPLEQQVDFTR 364 Query: 367 NPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEG 426 + V D+ WA+RKG FP VG RP GT+VIIEDV F ++ L+ + LF KHGY + Sbjct: 365 DAKVSDQLWAIRKGTFPAVGAVRPNGTTVIIEDVTFPIDQLSEGVTRLQALFVKHGYDDA 424 Query: 427 CIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPF 486 I+GHAL GN HF+ F A++ R+ AFM D+A +V ++ GS+KAEHGTGR +APF Sbjct: 425 IIFGHALEGNLHFVFPQGFDDPAEVARYEAFMQDVAQLVAVEFGGSLKAEHGTGRNMAPF 484 Query: 487 VEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECG 546 VE EWG DA+ LM IK++ DP+ +LNP V+L++D IH+KN+KP P D VDKCIECG Sbjct: 485 VELEWGHDAWQLMWQIKRLLDPENLLNPDVVLSEDPQIHLKNLKPLPEADPLVDKCIECG 544 Query: 547 FCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTI 606 FCE CP+ L SPRQRI R+I+ + G+ A++ +Y +DTCAA LC Sbjct: 545 FCEPVCPSEGLTLSPRQRIVIWRDIQARRRVGED--TAELEKAYQYHGLDTCAATGLCAQ 602 Query: 607 ACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGI 666 CPV + G LVRKLR+ T Q + + AKHF + + ++ G + Sbjct: 603 RCPVGINTGDLVRKLRSE--KATGQSMANQLAKHFAGALKATRFVLASASMAERLLGAPL 660 Query: 667 TNALMKTGRLIS-KEVPYWNPDFPKGGKL--PKPSPAKAGQETVVYFPACGGRTFGPTPK 723 L R +S V W+P P+ + PK G+ VVY AC RT GP Sbjct: 661 LTRLSGGVRKVSGGRVAQWDPSLPQPVRFVSPKAPEPSDGRPRVVYLAACVSRTMGPARG 720 Query: 724 DPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKM 783 D L +V LLE+ GY V+ PE LCCGQ + SKG A K+ ELI L + Sbjct: 721 DKAQEPLIDVTRRLLEKGGYQVVYPEALDSLCCGQPFASKGYPNQAATKKDELISALLRA 780 Query: 784 SNGGKIPVLVDALSCTYRTLTGNPQVQIT--DLVEFMHDKLLDKLSIN-KKVNVALHLGC 840 S G P+ D CT + + +T D V F+ D L ++L ++ +A+H+ C Sbjct: 781 SRNGVDPIYCDTSPCTLQIREAAEEAGLTLFDPVRFIRDHLYERLDFEPEQTPLAVHVTC 840 Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900 S + + + IA CS QV+ P GI CCG+AG+KG PE+NA +L+ + + Sbjct: 841 STQHLGESQGLIDIARRCSTQVVVPEGIHCCGFAGDKGFNVPELNAHSLKTLAEQ-TAGC 899 Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 +EG +R CE+GL++HSGI Y L YL++ +R Sbjct: 900 EEGISTSRTCEIGLSRHSGIDYHGLVYLVDRVTR 933 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: 2134 Number of extensions: 76 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: 938 Length adjustment: 43 Effective length of query: 891 Effective length of database: 895 Effective search space: 797445 Effective search space used: 797445 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