Alignments for a candidate for D-LDH in Marinobacter guineae M3B

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Marinobacter guineae M3B

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_099617893.1 CLH62_RS09330 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_002744735.1:WP_099617893.1
          Length = 938

 Score =  766 bits (1978), Expect = 0.0
 Identities = 413/931 (44%), Positives = 572/931 (61%), Gaps = 16/931 (1%)

Query: 8   VINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAP 67
           V+ ++R ++ D  V DDPV   A+ TDAS++R++P VVV  +   +V   L +ARKH  P
Sbjct: 7   VLAEIRQRIPDNRVFDDPVSTLAFGTDASFYRLIPRVVVRVQDEGEVVDLLALARKHQVP 66

Query: 68  VTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNR 127
           VTFRAAGTSLSGQAI + IL++LG D +   E+  + +QI L   VIG+ ANA LAP   
Sbjct: 67  VTFRAAGTSLSGQAISDSILIVLG-DQWNGHEIRDNGRQIRLQPGVIGAQANAWLAPRGY 125

Query: 128 KIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAE 187
           KIGPDPA+I + KIGGIVANNASGMCCGTAQNSY T+A  +L+  DG  +DT    S A 
Sbjct: 126 KIGPDPASINACKIGGIVANNASGMCCGTAQNSYHTLAGMRLVLVDGAVVDTENAASVAA 185

Query: 188 FAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLM 247
           F  +HG+LL  L +L+  TR+N  LA+RIR KY +KNTTG  +NSL+DF+DP +I+ HLM
Sbjct: 186 FRNSHGELLAALKKLAINTRNNRELADRIRHKYRLKNTTGLSLNSLVDFSDPLEILTHLM 245

Query: 248 VGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSI 307
           VG EG L F++ VTY+TV E   KA+A+ VF ++E   RA  ++  + V+A ELLD  S+
Sbjct: 246 VGSEGILGFVSAVTYNTVPEYPDKATALLVFRDVETCCRAASVLKTQPVAAVELLDRRSL 305

Query: 308 KAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTN 367
           ++V  KPG+PDW+  L   +  LL+ESRA     LE     +   LAGF   + ++F+ +
Sbjct: 306 RSVQDKPGLPDWIHGLSEGACALLVESRAPGPDVLEEQLAHIREALAGFPLEQQVDFTRD 365

Query: 368 PAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGC 427
             V  + WA+RKG FP VG  RP GT+VIIEDV F ++ LA     + +LF KHGY +  
Sbjct: 366 AGVSGQLWAIRKGTFPAVGAVRPNGTTVIIEDVTFPIDQLAEGVTRLQQLFVKHGYNDAI 425

Query: 428 IYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFV 487
           I+GHAL GN HF+    F   A++ R+ AFM D+A +V  ++ GS+KAEHGTGR +APFV
Sbjct: 426 IFGHALEGNLHFVFPQGFGDPAEVARYEAFMADVAQLVAVEFGGSLKAEHGTGRNMAPFV 485

Query: 488 EKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGF 547
           E EWG +A+ LM  IK++ DP  +LNP V+L++D  IH+KN+KP P  D  VDKCIECGF
Sbjct: 486 ELEWGHEAWQLMWRIKRLLDPDNLLNPDVVLSEDPRIHLKNLKPLPEADPLVDKCIECGF 545

Query: 548 CEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIA 607
           CE  CP+  L  SPRQRI   R+I+   ++G+     ++    +Y  +DTCAA  LC   
Sbjct: 546 CEPVCPSEGLTLSPRQRIVIWRDIQARRRAGED--TRELEKSWQYHGLDTCAATGLCAQR 603

Query: 608 CPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGV--IHKITGDG 665
           CPV  + G LVRKLR+     + Q V +  A+HF A   + +T F + G   + ++ G  
Sbjct: 604 CPVGINTGDLVRKLRSE--KASGQAVANQLARHFSAA--LKATRFVLAGASGVERLLGAP 659

Query: 666 ITNALMKTGRLISKE-VPYWNPDFPKGGK--LPKPSPAKAGQETVVYFPACGGRTFGPTP 722
           +   L    R +S + V  W+P  P+  +  +P P  A   +  VVY PAC  RT GP  
Sbjct: 660 LLTRLSAGVRKVSGDRVAQWDPSMPQPVRFVMPVPGSADDRRPRVVYLPACVSRTMGPAR 719

Query: 723 KDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSK 782
            D    +L  V   LLE+ GY V+ P+    LCCGQ + SKG  + A  K+ ELI  L +
Sbjct: 720 GDKAQDSLMAVTRRLLEKGGYQVVFPDTPDSLCCGQPFASKGYPEQAAGKKDELIGALLR 779

Query: 783 MSNGGKIPVLVDALSCT--YRTLTGNPQVQITDLVEFMHDKLLDKLSIN-KKVNVALHLG 839
            S  G  PV  D   CT   R       + + D V+F+ + LL++L+   ++  +A+H+ 
Sbjct: 780 ASRNGVDPVYCDTSPCTLQIREAAAEAGLALFDPVKFIREHLLERLAFEPEQTPLAVHVT 839

Query: 840 CSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVE 899
           CS + +     +  IA  CS +V+ P GI CCG+AG+KG   PE+NA ALR + +     
Sbjct: 840 CSTQHLGEAEGLIDIARRCSTKVVVPEGIHCCGFAGDKGFNVPELNAHALRTLPEQ-TAG 898

Query: 900 VKEGYYANRMCEVGLTQHSGISYRHLAYLLE 930
             EG   +R CE+GL++HSG+ Y  L YL++
Sbjct: 899 CAEGISTSRTCEIGLSRHSGLDYHGLVYLVD 929


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: 2114
Number of extensions: 81
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: 938
Length adjustment: 43
Effective length of query: 891
Effective length of database: 895
Effective search space:   797445
Effective search space used:   797445
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