GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS25120
          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:

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