GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Pseudomonas fluorescens FW300-N2C3

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate AO356_07570 AO356_07570 4Fe-4S ferredoxin

Query= uniprot:Q8EGS3
         (934 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07570 AO356_07570 4Fe-4S
           ferredoxin
          Length = 955

 Score =  770 bits (1989), Expect = 0.0
 Identities = 408/931 (43%), Positives = 573/931 (61%), Gaps = 11/931 (1%)

Query: 9   INDLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPV 68
           + D++  +  +   DDP+   A+ TDAS++R++P++VV  E+ ++V   L +A++   PV
Sbjct: 8   LRDVQQLIPQKRRFDDPLSTLAFGTDASFYRLIPKLVVRVESEDEVIALLKLAQRDQVPV 67

Query: 69  TFRAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRK 128
           TFRAAGTSLSGQAI + +L++LG D +   E+     QI L   VIG+ ANA LAP  RK
Sbjct: 68  TFRAAGTSLSGQAISDSVLIVLG-DNWNGREIREQGTQIRLQPGVIGAQANAWLAPFGRK 126

Query: 129 IGPDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEF 188
           IGPDPA+I + KIGGIVANNASGMCCGTAQN+Y T+A  +L+ ADGT LDT  + S A F
Sbjct: 127 IGPDPASINACKIGGIVANNASGMCCGTAQNTYHTLAGIRLVLADGTRLDTEDDNSVAAF 186

Query: 189 AKTHGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMV 248
             +HG+LL+ L+ L   TR N+ LA RIR KY +KNTTG  +N+L+DF +P DI++HL+V
Sbjct: 187 RTSHGELLERLATLGRETRANTELAARIRHKYRLKNTTGLSLNALVDFDEPVDILSHLLV 246

Query: 249 GMEGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGESVSAAELLDWPSIK 308
           G EGTL FI+ VTY+TV +   KASA+ VF ++E    A+ ++  + VSA ELLD  S++
Sbjct: 247 GSEGTLGFISAVTYNTVIDHPNKASALIVFPDVETCCNAVTVLKSQPVSAVELLDRRSLR 306

Query: 309 AVTGKPGMPDWLSELPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFSTNP 368
           +V  KPGMPD++  L   +  LLIESRA  +  L+     +   LAGF   + ++F+ +P
Sbjct: 307 SVQDKPGMPDFVQHLSINACALLIESRAASSSLLQEQLARIMTSLAGFPVEKQVDFTEDP 366

Query: 369 AVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPEGCI 428
               + WA+RK  FP VG  R  GT+VIIEDV F +E LA   + + ELF KH Y E  +
Sbjct: 367 RENARLWAIRKDTFPAVGAVRKTGTTVIIEDVTFPVEQLALGVNRLIELFDKHHYDEAIL 426

Query: 429 YGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAPFVE 488
           +GHAL GN HF+ T  F +  ++ R+ AFMDD+A +V  ++ GS+KAEHGTGR +APFVE
Sbjct: 427 FGHALEGNLHFVFTQGFNSAEEVARYQAFMDDVAHLVAVEFGGSLKAEHGTGRNMAPFVE 486

Query: 489 KEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIECGFC 548
            EWG DAY LM  +K++ DP GILNP V+L++D  IH+K++KP P  D+ VDKCIECGFC
Sbjct: 487 LEWGSDAYQLMWQLKRLLDPNGILNPDVVLSEDPQIHLKHLKPLPAADEIVDKCIECGFC 546

Query: 549 EKTCPTSALNFSPRQRIATLREIERLEQSGDKAAAAKMRADAKYDVIDTCAACQLCTIAC 608
           E  CP+  L  SPRQRI   R+I+  +++G      ++    +Y  IDTCAA  LC   C
Sbjct: 547 EPVCPSKDLTLSPRQRIVIWRDIQAKKRAG--TDTTELERAYQYQGIDTCAATGLCAQRC 604

Query: 609 PVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITG-DGIT 667
           PV  + G+LV+KLR+     T+ K  ++   +F    Q       V      + G   + 
Sbjct: 605 PVGINTGELVKKLRSR--DATKTKTANWIEGNFATTLQGARFALHVANGARMLLGAPRLA 662

Query: 668 NALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQE-TVVYFPACGGRTFGPTPKDPD 726
                  RL   +VP W    P+  K  + SP  + +   VVY  AC  R  GPT  D +
Sbjct: 663 KLSASLTRLSKGQVPQWTNAMPQPEKAIRFSPTVSDERPRVVYLAACVSRVMGPTAADKE 722

Query: 727 NRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKMSNG 786
             +L +   +LLE+AGY V+ P+    LCCGQ + SKG  + A+ KRQELI  L   S G
Sbjct: 723 QMSLYDKTRSLLEKAGYQVVFPDNVDSLCCGQPFASKGYTEQAEHKRQELIGALLHASRG 782

Query: 787 GKIPVLVDALSCTYRTL--TGNPQVQITDLVEFMHDKLLDKLS-INKKVNVALHLGCSAR 843
           G  P+  D   CT R +   G+ ++ + D V F+   L+++L  I ++  +A+H+ CS +
Sbjct: 783 GLDPIYCDTSPCTLRLVQDLGDVRLDLYDPVRFIRTHLMERLDFIPQEAPIAVHVTCSTQ 842

Query: 844 KMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLIPVEVKEG 903
            +     +  +A  CS  V+ P GI CCG+AG+KG   PE+NA +LR +K  +     EG
Sbjct: 843 HLGESQALIDLARKCSKNVVIPEGIHCCGFAGDKGFTTPELNAHSLRTLKDAVQY-CTEG 901

Query: 904 YYANRMCEVGLTQHSGISYRHLAYLLEECSR 934
              +R CE+GLT+HS I Y  L YL++  +R
Sbjct: 902 ISTSRTCEIGLTRHSEIDYHGLVYLVDRVTR 932


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: 2033
Number of extensions: 71
Number of successful extensions: 9
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: 955
Length adjustment: 44
Effective length of query: 890
Effective length of database: 911
Effective search space:   810790
Effective search space used:   810790
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 preprint 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