Aligments for a candidate for D-LDH in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments for a candidate for D-LDH in Marinobacter adhaerens HP15

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate GFF4151 HP15_4091 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein

Query= uniprot:Q8EGS3
         (934 letters)



>lcl|FitnessBrowser__Marino:GFF4151 HP15_4091 oxidoreductase,
           FAD/iron-sulfur cluster-binding domain protein
          Length = 938

 Score =  765 bits (1975), Expect = 0.0
 Identities = 408/934 (43%), Positives = 565/934 (60%), Gaps = 12/934 (1%)

Query: 7   EVINDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNA 66
           EV+ ++R ++ +  V +DP+   A+ TDAS++R++P+VVV  +   +V   L +AR+H  
Sbjct: 6   EVLANIRQRIPENRVFNDPMSTLAFGTDASFYRLIPKVVVRVQDEAEVVDLLAIARRHKV 65

Query: 67  PVTFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLN 126
           PVTFRAAGTSLSGQAI + IL++LG D +   ++  + +QI L   VIG+ ANA LAP  
Sbjct: 66  PVTFRAAGTSLSGQAISDSILIVLG-DQWNGHDIREEGRQIRLQPGVIGAQANAWLAPKG 124

Query: 127 RKIGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKA 186
            KIGPDPA+I + KIGGIVANNASGMCCGTAQNSY T+A  +L+ ADG  LDT    S +
Sbjct: 125 FKIGPDPASINACKIGGIVANNASGMCCGTAQNSYHTLAGMRLVLADGAVLDTEDPASVS 184

Query: 187 EFAKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHL 246
            F  +HG LL  L +L+  TR N  LAERIR KY +KNTTG  +N+L+DFT P DI+ HL
Sbjct: 185 AFRDSHGDLLAALKKLAINTRENPELAERIRHKYRLKNTTGLSLNALVDFTCPLDILTHL 244

Query: 247 MVGMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPS 306
           MVG EGTL F++ VTY+TV E   KA+A+ VF + E   RA   +  + V+A ELLD  S
Sbjct: 245 MVGSEGTLGFVSAVTYNTVPEYPDKATALLVFRDAESCCRAASALRSQPVAAVELLDRRS 304

Query: 307 IKAVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFST 366
           +++V  KPG+PDW+ +L   +  LL+E+RA  ++ L+     +   LA F   + ++F+ 
Sbjct: 305 LRSVQYKPGLPDWIHDLSESACALLVETRASSSEILDEQLTRIRQALAEFPLEQQVDFTR 364

Query: 367 NPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEG 426
           +  V D+ WA+RKG FP VG  RP GT+VIIEDV F ++ L+     +  LF KHGY + 
Sbjct: 365 DAKVSDQLWAIRKGTFPAVGAVRPNGTTVIIEDVTFPIDQLSEGVTRLQALFVKHGYDDA 424

Query: 427 CIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPF 486
            I+GHAL GN HF+    F   A++ R+ AFM D+A +V  ++ GS+KAEHGTGR +APF
Sbjct: 425 IIFGHALEGNLHFVFPQGFDDPAEVARYEAFMQDVAQLVAVEFGGSLKAEHGTGRNMAPF 484

Query: 487 VEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECG 546
           VE EWG DA+ LM  IK++ DP+ +LNP V+L++D  IH+KN+KP P  D  VDKCIECG
Sbjct: 485 VELEWGHDAWQLMWQIKRLLDPENLLNPDVVLSEDPQIHLKNLKPLPEADPLVDKCIECG 544

Query: 547 FCEKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTI 606
           FCE  CP+  L  SPRQRI   R+I+   + G+    A++    +Y  +DTCAA  LC  
Sbjct: 545 FCEPVCPSEGLTLSPRQRIVIWRDIQARRRVGED--TAELEKAYQYHGLDTCAATGLCAQ 602

Query: 607 ACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGI 666
            CPV  + G LVRKLR+     T Q + +  AKHF    +          +  ++ G  +
Sbjct: 603 RCPVGINTGDLVRKLRSE--KATGQSMANQLAKHFAGALKATRFVLASASMAERLLGAPL 660

Query: 667 TNALMKTGRLIS-KEVPYWNPDFPKGGKL--PKPSPAKAGQETVVYFPACGGRTFGPTPK 723
              L    R +S   V  W+P  P+  +   PK      G+  VVY  AC  RT GP   
Sbjct: 661 LTRLSGGVRKVSGGRVAQWDPSLPQPVRFVSPKAPEPSDGRPRVVYLAACVSRTMGPARG 720

Query: 724 DPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKM 783
           D     L +V   LLE+ GY V+ PE    LCCGQ + SKG    A  K+ ELI  L + 
Sbjct: 721 DKAQEPLIDVTRRLLEKGGYQVVYPEALDSLCCGQPFASKGYPNQAATKKDELISALLRA 780

Query: 784 SNGGKIPVLVDALSCTYRTLTGNPQVQIT--DLVEFMHDKLLDKLSIN-KKVNVALHLGC 840
           S  G  P+  D   CT +      +  +T  D V F+ D L ++L    ++  +A+H+ C
Sbjct: 781 SRNGVDPIYCDTSPCTLQIREAAEEAGLTLFDPVRFIRDHLYERLDFEPEQTPLAVHVTC 840

Query: 841 SARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEV 900
           S + +     +  IA  CS QV+ P GI CCG+AG+KG   PE+NA +L+ + +      
Sbjct: 841 STQHLGESQGLIDIARRCSTQVVVPEGIHCCGFAGDKGFNVPELNAHSLKTLAEQ-TAGC 899

Query: 901 KEGYYANRMCEVGLTQHSGISYRHLAYLLEECSR 934
           +EG   +R CE+GL++HSGI Y  L YL++  +R
Sbjct: 900 EEGISTSRTCEIGLSRHSGIDYHGLVYLVDRVTR 933


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: 2134
Number of extensions: 76
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 17 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, or view the source code.

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