Alignments for a candidate for D-LDH in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Halomonas desiderata SP1

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_086511823.1 BZY95_RS20920 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_002151265.1:WP_086511823.1
          Length = 960

 Score =  761 bits (1966), Expect = 0.0
 Identities = 399/925 (43%), Positives = 568/925 (61%), Gaps = 17/925 (1%)

Query: 23  DDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAI 82
           DDP+R   + TDAS++R++P++VV     +++   L   R+   PVTFRAAGTSLSGQA+
Sbjct: 31  DDPLRTLTYGTDASFYRLIPKLVVRPADEDELMAVLAGCRRRGLPVTFRAAGTSLSGQAV 90

Query: 83  GEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIG 142
            + +L+ L  +G+R  EV  + + I L   VIG+ AN +LAP  RKIGPDPA+I S  +G
Sbjct: 91  TDSVLIQL-REGWRGHEVLDNGRSIRLQPGVIGARANQLLAPFGRKIGPDPASINSCMVG 149

Query: 143 GIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSEL 202
           GI ANNASGMCCGTAQNSY+T+   +++ ADGT LDT    S+  F ++H +L++ L  L
Sbjct: 150 GIAANNASGMCCGTAQNSYRTVRDMRVILADGTRLDTADPASREAFRRSHAELVEGLECL 209

Query: 203 SHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTY 262
           S  TR N+ALAE+IR KY +KNTTGY +NSL+DF D  +I+ HLM+G EGTL FI+ +TY
Sbjct: 210 SAETRANAALAEKIRHKYRLKNTTGYALNSLVDFDDGIEILKHLMIGSEGTLGFISTITY 269

Query: 263 HTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSE 322
            TV +   KA+A+    +M    RA   +    VSA EL+D  ++++V  +PGMP+ L  
Sbjct: 270 DTVIDEPHKAAALVFLPDMATTCRATIALKPAPVSAVELMDRAALRSVENRPGMPEGLKR 329

Query: 323 LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLF 382
           LP  +A LLI+ R +D   L+   + V A   G   + P+ F+    +Y+ YW +RKGLF
Sbjct: 330 LPEGAAALLIDVRGNDEAELQARLEAVQAIFEGIHTLEPVTFTREKGLYELYWKIRKGLF 389

Query: 383 PIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIIT 442
           P VG  R  GT+VIIEDVAF +E L      +T+ FH+HGYPE  ++GHAL GN HF+  
Sbjct: 390 PAVGAVRDTGTTVIIEDVAFPIERLDEGVLALTDAFHRHGYPEAILFGHALEGNLHFVFP 449

Query: 443 PAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNI 502
             F    +++R+ A MD++A +V  +Y GS+KAEHGTGR +AP+VE EWG +AY LM  I
Sbjct: 450 QGFEKPGEVERYQALMDEVAQLVGVEYGGSLKAEHGTGRNMAPYVELEWGPEAYALMWRI 509

Query: 503 KQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPR 562
           K +FDP+ +LNP VIL+ +  +H++N+KP P  D  VDKCIECGFCE  CP+  L  +PR
Sbjct: 510 KALFDPENLLNPDVILSRNPTLHLENLKPLPAADPIVDKCIECGFCEHVCPSRDLTLTPR 569

Query: 563 QRIATLREIERLEQSGDKAAA------AKMRADAKYDVIDTCAACQLCTIACPVDNSMGQ 616
           QRI   RE+ RLE  G   A        ++R D +Y   +TCA   LC   CPV  + G+
Sbjct: 570 QRIVAAREMARLEAMGTSLAGEEAERLERLREDYRYAGDETCAVDGLCATQCPVGINTGE 629

Query: 617 LVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGD-GITNALMKTGR 675
           L+R++R   ++     +     +HF    ++     ++ GV   + G+ G++       R
Sbjct: 630 LIREMRRERLA-PHADMARRVGRHFSGTTRLARGMLNLAGVGRAVLGEKGLSKVSGGITR 688

Query: 676 LISKEVPYWNPDFPKGG--KLPKPSPAKAG-QETVVYFPACGGRTFGPTPKDPDNRTLPE 732
           +   +VP W P  PK    ++ K  PA  G +E VVYFP+C  R FG    D + R++ E
Sbjct: 689 VSGGKVPQWVPTLPKAAPVRVLKRKPATDGVREKVVYFPSCATRVFGAGHGDGERRSIME 748

Query: 733 VVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVL 792
           + ++LLE+AG+ VI PE    LCCG  ++SKG F  A  K +EL   L   S  G+ P+L
Sbjct: 749 ITLSLLEKAGFEVIVPEMPGHLCCGMAFQSKGQFDEATHKARELNRELLVASQNGRYPIL 808

Query: 793 VDALSCTYRTLTG--NPQVQITDLVEFMHDKLLDKLSINK-KVNVALHLGCSARKMKLEP 849
            D   C    + G  + ++ + + V F H+ LL +L +      VA+H+ CS+  M L  
Sbjct: 809 SDTSPCVLH-MQGRLDERLTVQEPVAFAHEHLLPRLDVTPLDERVAVHVTCSSTHMGLGE 867

Query: 850 KMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRM 909
           +M A+A AC+ +V+ PA I CCG+AG+KGL  PE+NASAL+ + + +  E   GY  +R 
Sbjct: 868 RMVALARACAREVVVPAEITCCGFAGDKGLVTPELNASALKGLAEQVG-ECDAGYSNSRT 926

Query: 910 CEVGLTQHSGISYRHLAYLLEECSR 934
           CE+GL+ H GI YR +  LL+  SR
Sbjct: 927 CEIGLSLHGGIPYRSILSLLDRASR 951


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: 2066
Number of extensions: 85
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: 960
Length adjustment: 44
Effective length of query: 890
Effective length of database: 916
Effective search space:   815240
Effective search space used:   815240
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 24 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