Alignments for a candidate for D-LDH in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Desulfovibrio vulgaris Miyazaki F

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate 8501466 DvMF_2196 FAD linked oxidase domain protein (RefSeq)

Query= uniprot:Q8EGS3
         (934 letters)



>FitnessBrowser__Miya:8501466
          Length = 942

 Score =  824 bits (2128), Expect = 0.0
 Identities = 419/933 (44%), Positives = 598/933 (64%), Gaps = 9/933 (0%)

Query: 5   YKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKH 64
           Y+  + +L   +  R V  DP+R  A+ TDAS++R++P++VV     ++V   + +A KH
Sbjct: 6   YQAFLKELLEFIPRRNVFTDPLRTLAYGTDASFYRLIPKIVVDTHNEDEVVGVIKLANKH 65

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

Query: 125 LNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKS 184
             +KIGPDPA+I + KIGGIVANNASGMCCG A+NSY+T++  +++F DGT LDT   KS
Sbjct: 125 FGKKIGPDPASIDTCKIGGIVANNASGMCCGVAENSYKTLSHMRVVFHDGTVLDTSDTKS 184

Query: 185 KAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIIN 244
           +A F +TH +++  ++ +     +   LA+ I +K+ IKNTTGY +N+L+DF DPFDII 
Sbjct: 185 RAAFQRTHPEIVNGVAAMRAQIMNKPELADLITRKFKIKNTTGYSLNALVDFADPFDIIQ 244

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

Query: 305 PSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEF 364
            S+++V  KPGMPD L  LP  +A LL+E+RA D  TL+     +TA +     IRP+ F
Sbjct: 305 ASLRSVEDKPGMPDGLQGLPDDAAALLVETRAGDKGTLDDQIARITASINAIPKIRPVAF 364

Query: 365 STNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYP 424
           +  PA +   W +RKGLFP VG  R  GT+VIIEDVAF +  LA A  ++  LF KHGY 
Sbjct: 365 TDVPAEFGTLWNVRKGLFPAVGAVRKVGTTVIIEDVAFPIASLADATLELQTLFAKHGYS 424

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

Query: 485 PFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIE 544
           PFVE EWG+DA+ LM+ +K +FDP G+LNPGVI+N D+  H++N+KP P     +DKCIE
Sbjct: 485 PFVELEWGRDAFLLMRELKTLFDPYGLLNPGVIINPDAEAHIRNLKPLPAAHTVIDKCIE 544

Query: 545 CGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVI--DTCAACQ 602
           CGFCE  CP+  + F+PRQRI   REI R+ ++GD+ +    +  + YD +  +TCA   
Sbjct: 545 CGFCEPICPSRDVTFTPRQRIVGWREISRM-KAGDEKSGLLKQLFSGYDYLGDNTCATDG 603

Query: 603 LCTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKIT 662
           LC   CPV  + G  +++LR   +    QK  D+ A+H+G V + +S       ++H++ 
Sbjct: 604 LCATRCPVGINTGAFIKELRADKVGARAQKAADWVARHYGGVCRSVSVALTGADLLHRVL 663

Query: 663 GDGITNALMKTGRLIS-KEVPYWNPDFPKGGKLPKPSP-AKAGQETVVYFPACGGRTFGP 720
           G  + +   K  R++S K+ P W    P G   P  +P        VVYFP+C  R+ GP
Sbjct: 664 GTDVMDKGAKFLRVVSLKKAPLWTRAMPTGASAPAHAPRGPVSDRKVVYFPSCIARSMGP 723

Query: 721 TPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVL 780
              D     LP   + LL +AGY+V+ PEK  DLCCGQ +ESKG    AD K +EL + L
Sbjct: 724 ARDDEQRDPLPAKTIGLLLKAGYHVLFPEKLGDLCCGQPFESKGFKAQADMKAKELSEAL 783

Query: 781 SKMSNGGKIPVLVDALSCTYRTL-TGNPQVQITDLVEFMHDKLLDKLSINK-KVNVALHL 838
            K+S+ G IPVL D   C YR   T + ++++ + +EF  + L   L   K +  +A+H 
Sbjct: 784 LKVSDTGAIPVLCDTSPCLYRMKETLDRRLKLYEPIEFALEHLTQALDFRKAERTIAIHS 843

Query: 839 GCSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPV 898
            C+A K+ L  K + +A  C+ QV+ P  + CCG+AG++G   PE+NA AL+ +++ + +
Sbjct: 844 TCTAVKLGLPGKFKQLAELCAEQVIVPEDVFCCGFAGDRGFSFPELNAGALKELRRQVEI 903

Query: 899 EVKEGYYANRMCEVGLTQHSGISYRHLAYLLEE 931
             +EGY  +R CE+GL+ H  I YR++ YL++E
Sbjct: 904 -CEEGYSTSRTCEIGLSLHGKIPYRNILYLVDE 935


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: 2123
Number of extensions: 61
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: 942
Length adjustment: 43
Effective length of query: 891
Effective length of database: 899
Effective search space:   801009
Effective search space used:   801009
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)
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Protein sequences (fasta format)
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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