Alignments for a candidate for D-LDH in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Pseudomonas stutzeri RCH2

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate GFF922 Psest_0951 FAD/FMN-containing dehydrogenases

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__psRCH2:GFF922
          Length = 950

 Score =  773 bits (1996), Expect = 0.0
 Identities = 410/919 (44%), Positives = 571/919 (62%), Gaps = 14/919 (1%)

Query: 23  DDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAI 82
           DDP+   A+ TDAS++R++P++VV  E+  +V   L +A   N PVTFRAAGTSLSGQAI
Sbjct: 31  DDPLSTLAFGTDASFYRLIPKLVVRVESEAEVIALLKLAHAENVPVTFRAAGTSLSGQAI 90

Query: 83  GEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIG 142
            + +L++LG D +   E+ +  +QI L   VIG++ANAVLAP  RKIGPDPA+I +AKIG
Sbjct: 91  SDSVLIVLG-DNWNGREIRNGGEQIRLQPGVIGANANAVLAPFQRKIGPDPASINAAKIG 149

Query: 143 GIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSEL 202
           GIVANN+SGMCCGTAQN+Y+T+A  +++ ADGT +D+    S   F ++H  LL+ L+EL
Sbjct: 150 GIVANNSSGMCCGTAQNTYKTLAGLRVVLADGTVVDSEDAASVDAFRQSHAALLEQLAEL 209

Query: 203 SHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTY 262
              TR NS LA +IR KY +KNTTG+ +N+L+D+ +P DI+NHLMVG EGTL FI+ VTY
Sbjct: 210 GRETRANSELAAKIRHKYRLKNTTGFSLNALVDYDEPLDILNHLMVGSEGTLGFISAVTY 269

Query: 263 HTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSE 322
            TV +   KASA+ VF ++E    A+P++  + VSA ELLD  S+++V  K GMP+W+ E
Sbjct: 270 DTVPDHPHKASALVVFPDVETCCLAVPVLKQQPVSAVELLDRRSLRSVEHKVGMPEWVKE 329

Query: 323 LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLF 382
           L   +  LLIESRA     L      +   +A F   + ++FS +P +Y++ W +RK  F
Sbjct: 330 LSPTACALLIESRAASQSLLHEQINLIMTSIAHFPVEKQVDFSEDPVIYNQLWKIRKDTF 389

Query: 383 PIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIIT 442
           P VG  R  GT+VIIEDV F +E LA   + + EL  KH Y E  ++GHAL GN HF+ T
Sbjct: 390 PAVGAVRQTGTTVIIEDVTFPVERLAEGVNRLIELLDKHRYDEAILFGHALEGNLHFVFT 449

Query: 443 PAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNI 502
             F   A + R+ AFM ++A +V  ++ G++KAEHGTGR +APFVE EWG +AY LM  I
Sbjct: 450 QGFDDPAQVARYEAFMGEVAQLVAVEFGGALKAEHGTGRNMAPFVELEWGSEAYALMWKI 509

Query: 503 KQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPR 562
           K++ DP GILNP V+L++D +IH+KN+KP P  D+ VDKCIECGFCE  CP++ L  +PR
Sbjct: 510 KRLLDPTGILNPDVVLSEDPDIHLKNLKPMPAADEIVDKCIECGFCEPVCPSNGLTLTPR 569

Query: 563 QRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLR 622
           QRI   R+I+  +++G      ++     Y  I+TCAA  LC   CPV  + G L+RKLR
Sbjct: 570 QRIVIWRDIQARKRAG--VDTTEIERLYHYHGIETCAATGLCAQRCPVGINTGDLIRKLR 627

Query: 623 TPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISK-EV 681
               S T     ++ A HF    Q            H I G      L  T    SK  V
Sbjct: 628 GREASKT--GAANWLADHFATAVQGTRFMLHAANGAHIILGTKRLAKLSATMTNASKGRV 685

Query: 682 PYWNPDFPKGGK---LPKPSPAKAGQETVVYFPACGGRTFGPTPKDPDNRTLPEVVVTLL 738
           P W P  P+  +   LPKP+ A+  +  VVY  AC  R   P  +D +   L +   +LL
Sbjct: 686 PQWTPATPQPLQRLHLPKPT-AQDERPRVVYLAACVSRAMAPAARDQEQEPLLDKTRSLL 744

Query: 739 ERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDALSC 798
           E+AGY VI PE+  DLCCGQ + SKG  +  + KRQE++D L K S GG  P+  D   C
Sbjct: 745 EKAGYQVIFPEQLNDLCCGQPFASKGYAEQGERKRQEMLDALLKASRGGLDPIYCDTSPC 804

Query: 799 TYRTLTG--NPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGCSARKMKLEPKMQAIA 855
           T R + G  + ++ + D V F+   LLDKL  + ++  +A+H+ CS + +     +  IA
Sbjct: 805 TLRLVQGLTDQRLDLYDPVRFIRTYLLDKLDFVPQEKAIAVHVTCSTQHLGEAQALIDIA 864

Query: 856 NACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVGLT 915
             C+ +V+ P GI CCG+AG+KG   PE+N  ALR++K  + +   EG   +R CE+GL+
Sbjct: 865 RRCAKEVVVPEGIHCCGFAGDKGFTTPELNCHALRSLKDAVQI-CDEGISTSRTCEIGLS 923

Query: 916 QHSGISYRHLAYLLEECSR 934
           +H  I Y  L YL++  +R
Sbjct: 924 RHGEIDYHGLVYLVDRVTR 942


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: 2074
Number of extensions: 87
Number of successful extensions: 7
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: 950
Length adjustment: 44
Effective length of query: 890
Effective length of database: 906
Effective search space:   806340
Effective search space used:   806340
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.

Downloads

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

Related tools

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