Alignments for a candidate for D-LDH in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Pseudomonas simiae WCS417

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate GFF4713 PS417_24110 4Fe-4S ferredoxin

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__WCS417:GFF4713
          Length = 936

 Score =  755 bits (1950), Expect = 0.0
 Identities = 403/917 (43%), Positives = 558/917 (60%), Gaps = 11/917 (1%)

Query: 23  DDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAI 82
           DDP+   A+ TDAS++R++P++V+  E+ ++V   L  A++ +  VTFRAAGTSLSGQAI
Sbjct: 22  DDPLSTLAFGTDASFYRLIPQLVIRVESEDEVVALLQWAQRDHVAVTFRAAGTSLSGQAI 81

Query: 83  GEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIG 142
            + +L++LG D +   E+     QI L   VIG+ ANA LAP  RKIGPDPA+I + KIG
Sbjct: 82  SDSVLIVLG-DNWNGREIRGQGTQIRLQPGVIGAQANAWLAPFGRKIGPDPASINACKIG 140

Query: 143 GIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSEL 202
           GIVANNASGMCCGTAQN+Y T+A  +L+ ADG+ LDT    S   F + HG LL+ L+ L
Sbjct: 141 GIVANNASGMCCGTAQNTYHTLAGIRLVLADGSRLDTEDATSVKAFREQHGALLERLATL 200

Query: 203 SHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTY 262
              TR N+ LA +IR KY +KNTTG  +N+L+DF +P DI++HL+VG EGTL FI+ VTY
Sbjct: 201 GRETRANAELAAKIRHKYRLKNTTGLSLNALVDFDEPLDILSHLLVGSEGTLGFISAVTY 260

Query: 263 HTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSE 322
            TV +   KASA+ VF ++E    A+ ++  + VSA ELLD  S+++V  KPGMP ++ +
Sbjct: 261 DTVVDHPNKASALIVFPDVETCCNAVTVLKTQPVSAVELLDRRSMRSVQNKPGMPAFVQQ 320

Query: 323 LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLF 382
           L   +  LLIESRA  +  L      + A LA F   + ++F+ +P    + WA+RK  F
Sbjct: 321 LSENACALLIESRAASSSLLHEQLALIMASLAQFPVEKQVDFTEDPTENARLWAIRKDTF 380

Query: 383 PIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIIT 442
           P VG  R  GT+VIIEDV F +E LA   + + ELF KH Y E  ++GHAL GN HF+ T
Sbjct: 381 PAVGAVRKTGTTVIIEDVTFPVEQLAIGVNRLIELFDKHHYDEAILFGHALEGNLHFVFT 440

Query: 443 PAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNI 502
             F +  ++ R+ AFMDD+A +V  ++ GS+KAEHGTGR +APFVE EWG DAY LM  +
Sbjct: 441 QGFNSAEEVTRYQAFMDDVAQLVAVEFGGSLKAEHGTGRNMAPFVELEWGSDAYQLMWQL 500

Query: 503 KQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPR 562
           K++ DP GILNP V+L+ D  IH+K++KP P  D+ VDKCIECGFCE  CP+  L  SPR
Sbjct: 501 KRLLDPNGILNPDVVLSQDPQIHLKHLKPLPAADELVDKCIECGFCEPVCPSKGLTLSPR 560

Query: 563 QRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLR 622
           QRI   R+I+  +++G       + A   Y  IDTCAA  LC   CPV  + G LV+KLR
Sbjct: 561 QRIVIWRDIQAKKRAG--VDTTDLEAAYHYQGIDTCAATGLCAQRCPVGINTGDLVKKLR 618

Query: 623 TPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISK-EV 681
           +     T  K  ++ A HF    Q       V      + G      L  +   +SK ++
Sbjct: 619 SRDADRT--KTAEWLATHFSTALQGARFTLHVANGARMLLGAPRLAKLSASMTKLSKGQI 676

Query: 682 PYWNPDFPKGGKLPKPSPAKAGQE-TVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLLER 740
           P W    P+  K  + SPA   +   VVY  AC  R  GP   D +  +L +   +LLE+
Sbjct: 677 PQWTAAMPQPEKAIRFSPAVTDERPRVVYLAACVSRAMGPAAGDKEQMSLYDKTRSLLEK 736

Query: 741 AGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSCTY 800
           AGY V+ P+    LCCGQ + SKG  + A+ KRQELI  L   S GG  P+  D   CT 
Sbjct: 737 AGYQVVFPDNQDSLCCGQPFASKGYAEQAEHKRQELIGALLHASRGGLDPIYCDTSPCTL 796

Query: 801 RTL--TGNPQVQITDLVEFMHDKLLDKLSIN-KKVNVALHLGCSARKMKLEPKMQAIANA 857
           R +   G+ ++ + D V F+   L+D+L    ++  +A+H+ CS + +     +  +A  
Sbjct: 797 RLVQDLGDTRLDLYDPVRFIRTHLMDRLDFTPQEAPIAVHVTCSTQHLGESQALIDLARR 856

Query: 858 CSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLTQH 917
           CS  V+ P GI CCG+AG+KG   PE+NA +LR +K  +     EG   +R CE+GL+QH
Sbjct: 857 CSNTVVIPEGIHCCGFAGDKGFTTPELNAHSLRTLKDAVQY-CSEGISTSRTCEIGLSQH 915

Query: 918 SGISYRHLAYLLEECSR 934
            GI Y  L YL++  ++
Sbjct: 916 GGIDYHGLVYLVDRVTQ 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: 2019
Number of extensions: 77
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources