Alignments for a candidate for D-LDH in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Desulfovibrio vulgaris Hildenborough

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 209186 DVU0253 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein

Query= uniprot:Q8EGS3
         (934 letters)



>MicrobesOnline__882:209186
          Length = 941

 Score =  833 bits (2152), Expect = 0.0
 Identities = 430/934 (46%), Positives = 597/934 (63%), Gaps = 7/934 (0%)

Query: 5   YKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKH 64
           YK  +  L   +    V  DP+R  A+ TDAS++R++P+VVV   T ++V   L +A + 
Sbjct: 6   YKTFLRHLLECVPRERVFTDPLRTLAYGTDASFYRLIPKVVVDTHTEDEVVAILKLAHRM 65

Query: 65  NAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAP 124
             PVTFRAAGTSLSGQ++ + IL+ LG DG+RK  +  +A +I L   +IGS AN +LA 
Sbjct: 66  RLPVTFRAAGTSLSGQSVTDSILVRLG-DGWRKYAIFDNATKIRLQPGIIGSHANRLLAE 124

Query: 125 LNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKS 184
             +KIGPDPA+I +AKIGGIVANNASGMCCG A+NSY+T+   +L+ ADGT +DTG +KS
Sbjct: 125 FGKKIGPDPASIDTAKIGGIVANNASGMCCGVAENSYKTLHRMRLVLADGTVVDTGDDKS 184

Query: 185 KAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIIN 244
           +A F ++HG +L+ L+ L         LA+RIR K+ IKNTTGY +N+L+DF+DPF+I+ 
Sbjct: 185 RAAFGRSHGAILEGLAALRQRVLDTPGLADRIRHKFKIKNTTGYSLNALVDFSDPFEIMQ 244

Query: 245 HLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDW 304
           HLMVG EGTL FI+EVTYHTV E   KASA+ +F  + DA  A  ++ GE VSA EL+D 
Sbjct: 245 HLMVGSEGTLGFISEVTYHTVTEHPHKASALVIFPTIRDACEATTILRGEPVSAVELMDS 304

Query: 305 PSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEF 364
            ++ +V  KPGMP  L  L   +A LL+E+RA +   LE     +TA +     + P+EF
Sbjct: 305 AALCSVADKPGMPGCLIGLSGQAAALLVETRAAEKSKLEEQIARITASIDAIPKVGPVEF 364

Query: 365 STNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYP 424
           +  PA + K WA+RKGLFP VG  R  GT+VIIEDVAF +  LA A  ++  +F KHGY 
Sbjct: 365 TDIPAEFGKLWAVRKGLFPAVGAVRKVGTTVIIEDVAFPIARLADATVELQGMFAKHGYT 424

Query: 425 EGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVA 484
           E  I+GHAL GN HF+ T  F + A+I+R+ AFMDD+A MV+ +Y+GS+KAEHGTGR +A
Sbjct: 425 EAIIFGHALEGNLHFVFTQDFNSPAEIERYRAFMDDVATMVVERYDGSLKAEHGTGRNMA 484

Query: 485 PFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIE 544
           PFVE EWG DAY LMK IK +FDP G++NPGVI+N+D+  HVK++KP P     +DKCIE
Sbjct: 485 PFVEMEWGHDAYVLMKEIKTLFDPNGLMNPGVIINEDAEAHVKHLKPLPPAHSIIDKCIE 544

Query: 545 CGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAK-MRADAKYDVIDTCAACQL 603
           CGFCE  CP+  + F+PRQRI   REI R++   +K+   + + +   Y   DTCA   L
Sbjct: 545 CGFCEPVCPSRNVTFTPRQRIVGWREIRRMQDGAEKSRLLRELFSGYGYLGDDTCATDGL 604

Query: 604 CTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG 663
           C   CPV  + G  +++LR         +  D+ AKHFG V + ++T    + ++H + G
Sbjct: 605 CATRCPVGINTGSFIKELRADQTGKYATRSADWVAKHFGLVCRTVNTSLKTVDLLHGLVG 664

Query: 664 DGITNALMKTGRLIS-KEVPYWNPDFPKGGKLPKP-SPAKAGQETVVYFPACGGRTFGPT 721
             +        R++S K++P WN   P G  +P+    A      VVYFP+C  R+ GP 
Sbjct: 665 TDVMEKGSSFLRVVSLKKIPLWNRAMPGGSSVPRSGGMATVPGRRVVYFPSCIARSMGPA 724

Query: 722 PKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLS 781
             D +   LP   V+LL +AGY V+ PE+  DLCCGQ +ESKG    AD K +EL   L 
Sbjct: 725 RDDNERDPLPAKTVSLLIKAGYEVLFPERLGDLCCGQPFESKGFKAQADMKAKELDAALL 784

Query: 782 KMSNGGKIPVLVDALSCTYRTL-TGNPQVQITDLVEFMHDKLLDKLSINK-KVNVALHLG 839
           K+SN G+ PVL D   C  R   T + ++++ + +EF  + L DKL+  + +  VALH  
Sbjct: 785 KVSNDGEYPVLCDTSPCLMRMRETLDRRLKLYEPIEFALEHLTDKLTFTRLERKVALHAT 844

Query: 840 CSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVE 899
           C+ARKM LE K+  +A  C+ + + P  I CCG+AG++G   PE+NA AL  +++ +   
Sbjct: 845 CTARKMGLEGKLLQLAQLCATETVVPEDIYCCGFAGDRGFSFPELNAGALAGLREQVET- 903

Query: 900 VKEGYYANRMCEVGLTQHSGISYRHLAYLLEECS 933
             EGY  +R CEVGL+ H  I YR++ YL++E +
Sbjct: 904 CTEGYSTSRTCEVGLSLHGRIPYRNILYLVDEAT 937


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: 2082
Number of extensions: 88
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: 941
Length adjustment: 43
Effective length of query: 891
Effective length of database: 898
Effective search space:   800118
Effective search space used:   800118
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)
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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