Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_011386481.1 AMB_RS20900 FAD-binding oxidoreductase
Query= uniprot:Q8EGS3 (934 letters) >NCBI__GCF_000009985.1:WP_011386481.1 Length = 936 Score = 814 bits (2102), Expect = 0.0 Identities = 419/934 (44%), Positives = 577/934 (61%), Gaps = 7/934 (0%) Query: 4 NYKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARK 63 +Y ++ DL + + DP+RR A+ TDAS++R+VP+VV +VK L R+ Sbjct: 7 DYSALLQDLTGVMPVSRLITDPLRRLAYGTDASFYRLVPQVVAEVRDEAEVKGVLAACRR 66 Query: 64 HNAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLA 123 H APVTFRAAGTSLSGQA+ + +L+ILG G+ + V + K+I L VIG++AN LA Sbjct: 67 HGAPVTFRAAGTSLSGQAVSDSVLMILG-TGWTQAVVEDEGKRIRLQPGVIGAEANRRLA 125 Query: 124 PLNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEK 183 RKIGPDPA+I S KIGGI ANNASGMCCGT+ NSYQT+ S +L+ ADGT +DTG + Sbjct: 126 AFARKIGPDPASIDSCKIGGIAANNASGMCCGTSDNSYQTVMSMRLVLADGTLVDTGNPE 185 Query: 184 SKAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDII 243 S A F +H +LL L ++ R + LA RIR K++IKNTTGY +N+L+DFTDP DI+ Sbjct: 186 SVAAFRASHAELLSRLDDMGRRVRDDETLAGRIRHKFAIKNTTGYSLNALVDFTDPLDIL 245 Query: 244 NHLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLD 303 HLM+G EGTL FI E+TY TV E KASA+ +F ++ +A RA+ + VSA EL+D Sbjct: 246 THLMIGSEGTLGFIAEITYRTVPEHAHKASALLLFPDIAEACRAVVALKQAPVSAVELMD 305 Query: 304 WPSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPME 363 S++ V KPGMP + L LL+E+R + A+ L ++ L+G + P Sbjct: 306 RASLRCVEDKPGMPAQIRGLADGVTSLLVEARGETAEALAANLAEIGRVLSGVTTLFPPA 365 Query: 364 FSTNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGY 423 F+ +P Y W +RKGLFP +G R GT+VIIEDVAF +E LAAA D+ L KHGY Sbjct: 366 FTDDPYEYGTLWKIRKGLFPALGAVRKVGTTVIIEDVAFPIESLAAATTDLEHLCRKHGY 425 Query: 424 PEGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAV 483 E I+GHAL GN HF T F + ++DR+ FMD++A++V+NKY+GS+KAEHGTGR + Sbjct: 426 DEAIIFGHALDGNLHFTFTQDFGIKEEVDRYARFMDEVAELVVNKYDGSLKAEHGTGRNM 485 Query: 484 APFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCI 543 APFVE EWG +A LM +IK + DP G+LNPGV+L+ D H+ N+KP P D VD CI Sbjct: 486 APFVEMEWGTEATALMWDIKGLLDPLGLLNPGVLLDKDPRAHLNNLKPLPAADSLVDTCI 545 Query: 544 ECGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQL 603 ECGFCE+ CP+ L SPRQRI + REI R + + + + D Y IDTCAAC L Sbjct: 546 ECGFCERMCPSHGLTLSPRQRITSWREISRRTAANENSDELRRLYD--YQGIDTCAACGL 603 Query: 604 CTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG 663 C ACPV G+L + LR + + V + ++H+GA G ++ ++ G Sbjct: 604 CATACPVGIETGRLTKSLRGRRLGSGAHAVGQWASRHYGAAMAATRFGLGAAALVSRLAG 663 Query: 664 DGITNALMKTGRLIS-KEVPYWNPDFPKGGKLPKPSPAKAGQETVVYFPACGGRTFGPTP 722 A+ R +S P P P+ A +G E VVYFP C RT GP Sbjct: 664 PSAMAAMASGLRTLSGGRTPKLGEHLPTAADFAPPANAPSG-ERVVYFPTCAARTMGPAS 722 Query: 723 KDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSK 782 DP+ +LP V+ +L RAG+ V+ P+ +LCCGQ +ESKG ADAK EL L K Sbjct: 723 GDPEKDSLPTVMTRVLARAGFGVVIPDGVENLCCGQAFESKGLQATADAKAAELEAALFK 782 Query: 783 MSNGGKIPVLVDALSCTYRTLTG-NPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGC 840 S+ G++P+++DA +C +R T ++++ D VEF+HD L +LS + V +H+ C Sbjct: 783 ASDHGRLPIVMDASACAWRMKTYLGERLKVVDSVEFLHDAALPRLSPTPQDAPVLVHVNC 842 Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900 ARK L+ KM +A AC+ + P + CCG+AG+KG PE+N ALR++ +P Sbjct: 843 GARKQGLDDKMVGLAKACAKTAIVPEAVGCCGFAGDKGFTNPELNDHALRHLAPQVPQGC 902 Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934 + GY +NR CE+GL H+ + YR + YLL+ +R Sbjct: 903 EAGYSSNRTCEIGLADHADVPYRSIVYLLDRTTR 936 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: 2084 Number of extensions: 70 Number of successful extensions: 9 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: 936 Length adjustment: 43 Effective length of query: 891 Effective length of database: 893 Effective search space: 795663 Effective search space used: 795663 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