Alignments for a candidate for D-LDH in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Desulfitobacterium hafniense DCB-2

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_015944483.1 DHAF_RS16125 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000021925.1:WP_015944483.1
          Length = 978

 Score =  766 bits (1978), Expect = 0.0
 Identities = 393/920 (42%), Positives = 567/920 (61%), Gaps = 11/920 (1%)

Query: 24  DPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFRAAGTSLSGQAIG 83
           DP+    +  DAS++R++P++V+      ++   L ++++   PVTFR AGTSLSGQA+ 
Sbjct: 56  DPLYTLGYGIDASFYRLIPKIVIRVLNDAEMGEILRLSQRTKIPVTFRTAGTSLSGQALT 115

Query: 84  EGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGPDPATIASAKIGG 143
           + +LL+L    +R  ++    K+I+L   ++G +AN  L    RKIGPDPA+I    IGG
Sbjct: 116 DSVLLVL-QGSWRHYKIHDHGKKISLEPGILGVEANRYLRSYKRKIGPDPASIDHCMIGG 174

Query: 144 IVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKTHGKLLQDLSELS 203
           I ANNASGMCCGT+ NSY+T+   +++F DGT LDTG   S+  F +  G+L++ + E+ 
Sbjct: 175 IAANNASGMCCGTSDNSYKTVDEMRIIFDDGTVLDTGDSSSRQYFRERKGELIRQIEEIR 234

Query: 204 HLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGMEGTLAFINEVTYH 263
                +  L   I+KKY IKNTTGY IN+ +DF DP +II H+++G EGTL FI+E+TY 
Sbjct: 235 DELNADPDLVAMIKKKYKIKNTTGYSINAFVDFQDPIEIIKHILIGSEGTLGFISEITYK 294

Query: 264 TVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVTGKPGMPDWLSEL 323
           TV +   KASA+ ++ +M+ A RA+  ++ + V+AAE++D PS+++V   PGMPD+L  L
Sbjct: 295 TVVDYDHKASALIMYPDMDHACRAVMKLDRDLVAAAEMMDRPSLRSVEDAPGMPDYLKSL 354

Query: 324 PALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVYDKYWAMRKGLFP 383
              +  LL+E R  + + LE   ++ TA L     I P+ F++  + Y+ YW +RK +FP
Sbjct: 355 SDTATALLVEVRGANPEELEQRIKNATAVLEDIPTIFPISFTSVKSEYETYWKIRKDIFP 414

Query: 384 IVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGHALAGNFHFIITP 443
            VGG R +GT+V+IEDVAF LE LA A  D+ +  +K GY +  IYGHAL GN+HFI TP
Sbjct: 415 AVGGVRAQGTAVLIEDVAFPLERLAEATADLRDSLNKFGYTDAIIYGHALDGNWHFIFTP 474

Query: 444 AFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEWGQDAYTLMKNIK 503
            F +  +I R+   M+++ + V+ KYNGS+KAEHGTGR +APFVE EWG   Y LMK IK
Sbjct: 475 KFDSDEEIARYEGLMNEVNEFVVKKYNGSLKAEHGTGRNMAPFVELEWGSKTYELMKRIK 534

Query: 504 QVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKTCPTSALNFSPRQ 563
             FDP  +LNPGVI+ND+ N++++N+K  P   D +D+C  CGFC+  CP+  L  +PR 
Sbjct: 535 SAFDPHNLLNPGVIINDNKNVYLENLKAMPASHDTIDRCTNCGFCQDICPSKHLTTTPRM 594

Query: 564 RIATLREIERLEQSG-DKAAAAKMRADAKYDVIDTCAACQLCTIACPVDNSMGQLVRKLR 622
           RI   REI  L+++G D     ++  D  Y    TCA   LC  +CP++ + G   + LR
Sbjct: 595 RIILQREISDLKRTGRDPKRLMRLLRDYDYAGNATCATDGLCATSCPLNINTGDNTKYLR 654

Query: 623 TPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNALMKTGRLISK-EV 681
           +  I+   +KV    AK+   V  ++  G   +  +H   G  I   + +T R +S+ ++
Sbjct: 655 SRAITPATRKVARALAKNMNGVTGIMRFGLGAVDGVHGFLGTRILGGMARTARDVSQSKI 714

Query: 682 PYWNPDFPKGGK---LPKPSPAKA-GQET--VVYFPACGGRTFGPTPKDPDNRTLPEVVV 735
           P WN   P  GK    P+P  A A G E   VVYFP+C  R+ GP  KD D R L EV+ 
Sbjct: 715 PLWNEWMPSKGKGKVRPRPPFASAQGGEVLKVVYFPSCISRSMGPARKDKDQRPLNEVMC 774

Query: 736 TLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNGGKIPVLVDA 795
           +LL +AGY VI P     LCCG  WESKG F  AD K  EL  VL + S  GK P++ D 
Sbjct: 775 SLLAKAGYEVIIPPGLDKLCCGMPWESKGFFDIADEKSAELEKVLLQASENGKYPIVCDT 834

Query: 796 LSCTYRTLTG-NPQVQITDLVEFMHDKLLDKLSINK-KVNVALHLGCSARKMKLEPKMQA 853
             C YR        +++ + VEF HD LL +L I K +  +A+H+ CS+ KM+L  K +A
Sbjct: 835 SPCLYRMKRAFTSGIELHESVEFTHDFLLHRLKIKKARETIAVHVTCSSVKMRLSEKFKA 894

Query: 854 IANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEGYYANRMCEVG 913
           +A AC+ +V+ P  + CCG+AG+KG   PE+N +AL  +   +P     GY  +R CE+G
Sbjct: 895 LAEACAEKVIIPDDVHCCGFAGDKGFTYPELNDAALAGLNGALPDNCAGGYSNSRTCEIG 954

Query: 914 LTQHSGISYRHLAYLLEECS 933
           L+ HSGISY+ L YL++ CS
Sbjct: 955 LSAHSGISYQSLIYLVDRCS 974


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: 2025
Number of extensions: 74
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: 978
Length adjustment: 44
Effective length of query: 890
Effective length of database: 934
Effective search space:   831260
Effective search space used:   831260
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.

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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 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