GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF4151
          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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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:

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:

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:

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:

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