Alignments for a candidate for D-LDH in Desulfogranum mediterraneum DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Desulfogranum mediterraneum DSM 13871

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_035245159.1 G494_RS0101840 FAD-binding and (Fe-S)-binding domain-containing protein

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000429965.1:WP_035245159.1
          Length = 955

 Score =  809 bits (2090), Expect = 0.0
 Identities = 424/943 (44%), Positives = 593/943 (62%), Gaps = 20/943 (2%)

Query: 5   YKEVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKH 64
           Y+E    +R  +    +  DP+R   + TDAS++R++P++V++ E  +QV+L L  A + 
Sbjct: 9   YREFYRKIRAGIPAENIISDPLRTITFGTDASFYRLIPKLVINVEHEKQVQLILREAGRR 68

Query: 65  NAPVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAP 124
             PVTFRAAGTSLSGQAI + IL+ LG  G+   +V   A++I L   +IG  AN +LA 
Sbjct: 69  GLPVTFRAAGTSLSGQAISDSILVRLGK-GWNLYKVYDQARRIQLQPGIIGGQANRILAE 127

Query: 125 LNRKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKS 184
             RKIGPDPA+I +AKIGGI+ANNASGMCCG AQNSYQT+ S +++  DGT +DTG E S
Sbjct: 128 FGRKIGPDPASIDAAKIGGILANNASGMCCGVAQNSYQTLESMRIIMVDGTLVDTGDEAS 187

Query: 185 KAEFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIIN 244
            A+F ++HG +L  L+ L      +  L ERIR K+ IKNTTGY +N+L+DF++PF+I+ 
Sbjct: 188 MAKFRRSHGHILNRLTALREQVLSDPILTERIRYKFKIKNTTGYSLNALLDFSEPFEIMQ 247

Query: 245 HLMVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDW 304
           HL++G EGTL FI +V Y TV E   KASA+ ++ ++  A  A+P++  + VSAAEL+D 
Sbjct: 248 HLLIGSEGTLGFIADVVYRTVAEHPHKASALILYPDVRTACEAVPVLREQPVSAAELMDR 307

Query: 305 PSIKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEF 364
             + +V GKPG PD+L EL      LL+E+RAD ++ L    + + A L  F  +RP+EF
Sbjct: 308 AGLASVAGKPGKPDYLEELGPTVTALLVETRADSSKELSSQIERIQASLTPFPTVRPIEF 367

Query: 365 STNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYP 424
           +  P  +++ W +RKGLFP VG  R  GT+VIIEDVAF  EHLAAAA D+ +LF K+ Y 
Sbjct: 368 TAIPEEFNRLWTIRKGLFPAVGAVRETGTTVIIEDVAFPGEHLAAAALDLQQLFLKYHYH 427

Query: 425 EGCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVA 484
           E  I+GHAL GN HF+ T  F+ Q ++ R+  FMD++ ++V+ +Y+GS+KAEHGTGR +A
Sbjct: 428 EAIIFGHALDGNLHFVFTQDFSIQEEVVRYRRFMDEVVELVVEQYDGSLKAEHGTGRNMA 487

Query: 485 PFVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIE 544
           PFVEKEWG+ AYTLMK IK++FDP G+LNPGVILN D   H+KN+KP P   + VDKCIE
Sbjct: 488 PFVEKEWGEAAYTLMKEIKEIFDPAGLLNPGVILNSDLETHIKNLKPLPPTHELVDKCIE 547

Query: 545 CGFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADA-KYDVIDTCAACQL 603
           CGFCE  CP+  L FSPRQRI   REI R    G+ +   K    A +Y  +DTCAA  L
Sbjct: 548 CGFCEPVCPSKELTFSPRQRIVGRREISRRLALGENSPGVKELIKAYQYPGMDTCAADSL 607

Query: 604 CTIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG 663
           C+  CPV    G++++ LR         +V D  A HF  V++V+ T  + + ++HKI G
Sbjct: 608 CSSRCPVGIDTGKMIKALRQEANGPLANRVADQVADHFKLVSRVVGTTLNGVDILHKIAG 667

Query: 664 DGITNALMKTGRLISKE-VPYWNPDFPKGGKLPKPSPAKAGQE-----------TVVYFP 711
                 +    R  S + +P WN + P     P  +  KA QE            VVYFP
Sbjct: 668 SHQMETMAAVARKGSLDTLPLWNREMPTAP--PDITRNKAQQELQSALSQEDDSLVVYFP 725

Query: 712 ACGGRTF-GPTPKDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNAD 770
           +C  R   GP+  D D+  LP+   +LL +AGY V+ PE    LCCGQ +ESKG    AD
Sbjct: 726 SCASRAMGGPSRSDRDHLPLPQQTASLLGKAGYRVLYPENLAALCCGQAFESKGFLGQAD 785

Query: 771 AKRQELIDVLSKMSNGGKIPVLVDALSCTYR-TLTGNPQVQITDLVEFMHDKLLDKLSIN 829
            K  EL   L K+SN G IP+L D   C YR   T +  +++ + +EF+   L+++L   
Sbjct: 786 RKSAELNQALLKISNKGAIPILCDTSPCLYRMRSTLDQDLKLYEPIEFVLLFLMERLRFT 845

Query: 830 KKV-NVALHLGCSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASA 888
           +K   +A+H  CS RKM LE  ++ +A  C+ +V+ P  I CCG+AG++G   P++N SA
Sbjct: 846 QKERKIAVHPTCSTRKMGLEGALRQLAEKCATEVVWPEDIFCCGFAGDRGFTFPQLNRSA 905

Query: 889 LRNIKKLIPVEVKEGYYANRMCEVGLTQHSGISYRHLAYLLEE 931
           L  +K+ +      GY  ++ CE+GL+ H  I YR +  L++E
Sbjct: 906 LDGLKEEV-AGCSAGYSTSKTCEIGLSLHGEIPYRSILELVDE 947


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: 1928
Number of extensions: 74
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: 955
Length adjustment: 44
Effective length of query: 890
Effective length of database: 911
Effective search space:   810790
Effective search space used:   810790
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 Apr 09 2024. 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 2024 update 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