Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate PP_4737 PP_4737 D-lactate dehydrogenase
Query= uniprot:Q8EGS3 (934 letters) >FitnessBrowser__Putida:PP_4737 Length = 936 Score = 776 bits (2005), Expect = 0.0 Identities = 411/917 (44%), Positives = 563/917 (61%), Gaps = 11/917 (1%) Query: 23 DDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAI 82 DDP A+ TDAS++R++P++VV E+ ++V + +A++ PVTFRAAGTSLSGQAI Sbjct: 22 DDPTSTLAFGTDASFYRLIPKLVVRVESEDEVVGLIKLAQRERVPVTFRAAGTSLSGQAI 81 Query: 83 GEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIG 142 + +L++LG D + E+ +QI L VIG+ ANA LAP RKIGPDPA+I + KIG Sbjct: 82 SDSVLIVLG-DNWNGREIRRQGEQIRLQPGVIGAQANAWLAPFGRKIGPDPASINACKIG 140 Query: 143 GIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSEL 202 GIVANNASGMCCGTAQN+Y T+A +L+ ADGT LD+ S A F +H +LL+ L+ L Sbjct: 141 GIVANNASGMCCGTAQNTYHTLAGLRLVLADGTRLDSEDPASVAAFESSHAELLEALARL 200 Query: 203 SHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTY 262 TR N+ALAERIR KY +KNTTG +N+L+D+ P DI+ HL+VG EGTL FI+ VTY Sbjct: 201 GRETRANTALAERIRHKYRLKNTTGLSLNALVDYDQPLDILQHLLVGSEGTLGFISAVTY 260 Query: 263 HTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSE 322 TV + KASA+ VF ++E RA+P++ + VSA ELLD S+++V PGMP W+ Sbjct: 261 DTVPDHPHKASALLVFPSVESCCRAVPVLKQQPVSAVELLDRRSLRSVQNMPGMPLWVKG 320 Query: 323 LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLF 382 L + LLIESRA L Q + A +A F + ++FS +PAVY++ W +RK F Sbjct: 321 LSDNACALLIESRAASQSLLHEQLQQIMASIADFPLEQQVDFSEDPAVYNQLWKIRKDTF 380 Query: 383 PIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIIT 442 P VG R GT+VIIEDV F +E LA + + +LF KH Y E I+GHAL GN HF+ T Sbjct: 381 PAVGAVRQTGTTVIIEDVTFPVEQLAEGVNRLIQLFDKHHYDEAIIFGHALEGNLHFVFT 440 Query: 443 PAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNI 502 F + ++ R+ AFMDD+A +V ++ GS+KAEHGTGR +APFVE EWG DAY LM + Sbjct: 441 QGFNSAEEVARYQAFMDDVAQLVAVEFGGSLKAEHGTGRNMAPFVELEWGHDAYQLMWKL 500 Query: 503 KQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPR 562 K++ DP GILNP V+L++D +IH+KN+KP P D VDKCIECGFCE CP+ L SPR Sbjct: 501 KRLLDPNGILNPDVVLSEDPDIHLKNLKPLPAADKIVDKCIECGFCEPVCPSKGLTLSPR 560 Query: 563 QRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLR 622 QRI R+I+ +++G ++ +Y IDTCAA LC CPV + G+LV+KLR Sbjct: 561 QRIVMWRDIQAKQRAG--IDTRELMQSYQYQGIDTCAATGLCAQRCPVGINTGELVKKLR 618 Query: 623 TPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISK-EV 681 + + K D+ A+HF K+ G L + SK + Sbjct: 619 SQ--AADHAKTADWLAEHFHTALSGARLTLTAANTARKLLGAPRLGRLSASLSKASKGRL 676 Query: 682 PYWNPDFPKGGK-LPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLER 740 P W P P+ + L + + + VVY AC R GP D + +L + LLE+ Sbjct: 677 PQWTPAMPQPLRPLAFGATSNDARPRVVYLAACVSRVMGPAYADREQSSLLDKTRALLEK 736 Query: 741 AGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTY 800 AGY V+ P+ LCCGQ + SKG + A+ KRQELI L S GG P+ D CT Sbjct: 737 AGYQVVFPDNADSLCCGQPFASKGYPEQAEHKRQELITALLHASRGGLDPIYCDTSPCTL 796 Query: 801 RTL--TGNPQVQITDLVEFMHDKLLDKLSINKKVN-VALHLGCSARKMKLEPKMQAIANA 857 R + + ++ + D V F+ LLD+L + VA+H+ CS + + + +A Sbjct: 797 RLVQDLSDTRLDLYDPVRFIRTHLLDRLEFTPQDEPVAVHVTCSTQHLGESQALIDLARR 856 Query: 858 CSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLTQH 917 CS QV+ P GI CCG+AG+KG PE+NA +LR++K + EG +R CE+GL+ H Sbjct: 857 CSKQVVIPEGIHCCGFAGDKGFTTPELNAHSLRSLKDAVQY-CSEGISTSRTCEIGLSSH 915 Query: 918 SGISYRHLAYLLEECSR 934 SGI Y L YL++ +R Sbjct: 916 SGIDYHGLVYLVDRVTR 932 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: 2023 Number of extensions: 79 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: 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