GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07570
          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:

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