GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Azospirillum brasilense Sp245

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate AZOBR_RS25120 AZOBR_RS25120 4Fe-4S ferredoxin

Query= uniprot:Q8EGS3
         (934 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS25120 AZOBR_RS25120 4Fe-4S
           ferredoxin
          Length = 962

 Score =  845 bits (2184), Expect = 0.0
 Identities = 439/934 (47%), Positives = 591/934 (63%), Gaps = 13/934 (1%)

Query: 12  LRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTFR 71
           LR  + D  +  DP+R  A+ TD S++R++P++V   E   +V   L + R+   PVTFR
Sbjct: 13  LREFMPDERLVTDPLRTLAYGTDGSFYRLIPKIVAIVEAEGEVVRLLNLCRELKTPVTFR 72

Query: 72  AAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIGP 131
           AAGTSLSGQA+ + +L++LG D +R   +   A  +TL   VIG++AN  LAP  RKIGP
Sbjct: 73  AAGTSLSGQAVTDSVLVLLG-DSWRGCTIPPGAATVTLQPGVIGAEANRKLAPFGRKIGP 131

Query: 132 DPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAKT 191
           DPA+IA+AKIGGI ANNASGMCCGTAQNSY+T+AS +L+ ADGT LDTG   S+A FA +
Sbjct: 132 DPASIATAKIGGIAANNASGMCCGTAQNSYRTLASMRLVLADGTLLDTGDAASRAAFAVS 191

Query: 192 HGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGME 251
           HG LL  LS+L+  TR +  LAERIR K+ IKNTTGY +N+L+DF +P +I+ HLM+G E
Sbjct: 192 HGALLSGLSDLAARTRADDKLAERIRNKFRIKNTTGYSLNALVDFEEPVEILQHLMIGSE 251

Query: 252 GTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIKAVT 311
           GTL F++E+TY+TV E   KA+A+ ++ ++ +A RA+ L+    VSA EL+D  S+++V 
Sbjct: 252 GTLGFLSEITYNTVPEHAHKANALLMYPDIGEACRAVALMKPTPVSAVELMDRASLRSVE 311

Query: 312 GKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNPAVY 371
           GKPGMPD++  L   ++ LL+E R +DA  L+     V+A +A    + P  F+T+  + 
Sbjct: 312 GKPGMPDFIGGLGPDASALLVEIRGEDAAALDANIAAVSAVIAQTQTLFPPTFTTDAKLG 371

Query: 372 DKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCIYGH 431
           + YW +RKGLFP VG  R  GT+VIIEDVA+ L+ LA A  ++  +F K GY E  I+GH
Sbjct: 372 ESYWKIRKGLFPAVGAMRKVGTTVIIEDVAYPLDRLAEATVELQAMFLKFGYTEAIIFGH 431

Query: 432 ALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVEKEW 491
           AL GN HF+ T AF T  ++DR+  FMD + D V+ KY+GS+KAEHGTGR +APFVE EW
Sbjct: 432 ALEGNLHFVFTQAFDTDEEVDRYRRFMDAVCDQVVRKYDGSLKAEHGTGRNMAPFVEMEW 491

Query: 492 GQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFCEKT 551
           G  AY LMK IK + DPQG+LNPGVILNDD   H+KN+K  P     VD CIECGFCE T
Sbjct: 492 GPQAYGLMKEIKALLDPQGLLNPGVILNDDPEAHLKNLKAMPAAHPLVDTCIECGFCEPT 551

Query: 552 CPTSALNFSPRQRIATLREIERLEQSG-DKAAAAKMRADAKYDVIDTCAACQLCTIACPV 610
           CP+  +  SPRQRI   REI RLE +G D A    +     Y  IDTCAAC LC+ ACPV
Sbjct: 552 CPSHKMTLSPRQRIVGWREISRLEATGADAARLGALHEAYDYQGIDTCAACGLCSTACPV 611

Query: 611 DNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGDGITNAL 670
               G L++ +R     T  Q    + A+H      V  TG  +  +  +  GD   N L
Sbjct: 612 GIETGLLIKAIRGDRRGTMAQGFGTYVAEHTAGALSVARTGLKLADLAKRTLGDDTANGL 671

Query: 671 M-KTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQE-------TVVYFPACGGRTFGPTP 722
             K   +  + +P+     P          AKA  +       TVVY P+C  R+ GP  
Sbjct: 672 FEKLRNVTGQRLPHLPRALPTPTNFTPLPQAKASADAPTANTPTVVYVPSCTSRSMGPAA 731

Query: 723 KDPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSK 782
            DP+   LP  V  L ++AGY V  PE+   LCCG   ESKG    ADAK +E++  +  
Sbjct: 732 NDPEKTPLPVKVEALFQKAGYRVAYPEQLASLCCGMPLESKGLAAQADAKAEEMVRAIWA 791

Query: 783 MSNGGKIPVLVDALSCTYRTL--TGNPQVQITDLVEFMHDKLLDKLSINKKVN-VALHLG 839
            S  G  PV++D   C++R      +  +Q+ DLVEF+HD LLD+L+  K+   V LHL 
Sbjct: 792 ASADGTAPVVLDTSPCSFRLKKHLKDAGLQVLDLVEFIHDHLLDRLNFTKQTEPVVLHLT 851

Query: 840 CSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVE 899
           CS R+M L+ KM+A+A AC+ QV+ P  + CCG+AG+KG   PE+NA ALR++ K IP  
Sbjct: 852 CSTRRMGLDAKMKAVAAACATQVVVPEDVGCCGFAGDKGFTTPELNAHALRHLSKDIPAG 911

Query: 900 VKEGYYANRMCEVGLTQHSGISYRHLAYLLEECS 933
            K GY  +R CE+GL+ HSG+ YR + YL++ CS
Sbjct: 912 AKAGYSNSRTCEIGLSDHSGLPYRSIVYLVDACS 945


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: 2207
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: 962
Length adjustment: 44
Effective length of query: 890
Effective length of database: 918
Effective search space:   817020
Effective search space used:   817020
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 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