GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Pseudomonas putida KT2440

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)



>lcl|FitnessBrowser__Putida:PP_4737 PP_4737 D-lactate dehydrogenase
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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