GapMind for catabolism of small carbon sources

 

Aligments for a candidate for odc in Azospirillum brasilense Sp245

Align ornithine decarboxylase, degradative (EC 4.1.1.17) (characterized)
to candidate AZOBR_RS27535 AZOBR_RS27535 amino acid decarboxylase

Query= ecocyc::ORNDECARBOXDEG-MONOMER
         (732 letters)



>FitnessBrowser__azobra:AZOBR_RS27535
          Length = 785

 Score =  593 bits (1528), Expect = e-173
 Identities = 316/698 (45%), Positives = 417/698 (59%), Gaps = 28/698 (4%)

Query: 55  GYGIPVFIATENQ--ERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFF 112
           G  +P+ +    Q  E +P + L ++ G     E   EF  + L +    Y   L+ PFF
Sbjct: 86  GLEMPIILLVRRQRLENIPVDVLNQVDGYVFLAEETPEFIAKNLVSRLKQYAETLKTPFF 145

Query: 113 RALVDYVNQGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIH 172
             LVDY  +GN  + CPGH GG F+ R P G  FVE+ GEA+FR D+ N+ + MGDLL+H
Sbjct: 146 GELVDYAEEGNQLWTCPGHNGGIFYSRSPIGRIFVEHLGEAVFRDDIDNSVLEMGDLLVH 205

Query: 173 EGAPCIAQQHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGAL 232
           EG    AQ+ AAK+F A++TYFVLNGTS+SNK+VL+AL+   DLVLFDRNNHK+ HHG L
Sbjct: 206 EGPALKAQKEAAKIFGAERTYFVLNGTSASNKIVLSALVAEDDLVLFDRNNHKAAHHGGL 265

Query: 233 LQAGATPVYLETARNPYGFIGGIDAHCFEESYLRELI----AEVAPQRAKEARPFRLAVI 288
              G  PV+LET RN YG IG ID    +E  +R  I        P   K  RPFR AVI
Sbjct: 266 FLGGGIPVFLETDRNAYGLIGPIDHEALDEERIRAKIRGNPLVKDPDAWKRERPFRAAVI 325

Query: 289 QLGTYDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLD-LNENDPGI 347
           Q  +YDGTIY+A  ++ KIGHLCDYILFD AW G+ +F P+      + LD L++  PGI
Sbjct: 326 QQCSYDGTIYSAETILAKIGHLCDYILFDEAWAGFLKFHPLFKGRFAMGLDGLHDGHPGI 385

Query: 348 LVTQSVHKQQAGFSQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNI 407
           + TQS HKQ A FSQ SQIH KDSHI+GQ+R V H+R N  F++HASTSPFYPLFA+L++
Sbjct: 386 IATQSTHKQLASFSQASQIHVKDSHIRGQRRRVEHRRFNETFLLHASTSPFYPLFASLDV 445

Query: 408 NAKMHEGVSGRNMWMDCVVNGINARKLILDNCQHIR-------------PFVPELV--DG 452
            A+M +G SG  +W D +  G+  RK I    +                PFVP+ V  DG
Sbjct: 446 GAQMMKGRSGEVLWDDTIRLGVELRKKIRAIRREFEERESAPARRWFFDPFVPDRVSFDG 505

Query: 453 K--PWQSYETAQIAVDLRFFQFVPGEHWHSFEGYAENQYFVDPCKLLLTTPGIDARNGEY 510
               W+   T  +A D+R + F PG HWH F   A      DP KL L TPG D R G Y
Sbjct: 506 AEIAWEEVPTDALASDVRHWVFKPGAHWHGFRHVAAGYAMTDPNKLTLLTPGFDRRTGAY 565

Query: 511 EAFGVPATILANFLRENGVVPEKCDLNSILFLLTPAEDMAKLQQLVALLVRFEKLLESDA 570
           E  G+PA ++A +LREN +VPEK DLNSILFLLTP  + +K   L++ LV F++L + +A
Sbjct: 566 EEHGIPAPVVAQYLRENRIVPEKNDLNSILFLLTPGVESSKAGTLLSALVAFKRLHDDNA 625

Query: 571 PLAEVLPSIYKQHEERYAGYTLRQLCQEMHDLYARHNVKQLQKEMFRKEHFPRVSMNPQE 630
            L +V+P    +   RYAG  LR LC EMH  Y      +LQ+ MFR +H P + M P+E
Sbjct: 626 LLEDVIPEFVARRPARYAGRRLRDLCAEMHGFYRERRTNELQRRMFRPDHLPEMVMPPRE 685

Query: 631 ANYAYLRGEVELVRLPDAEGRIAAEGALPYPPGVLCVVPGEIW---GGAVLRYFSALEEG 687
           A    +R +V+ + +    GR+A    + YPPG+  +VPGE        ++ Y    +EG
Sbjct: 686 AVRRLVRNDVDYLPIDRIAGRVATTLFVVYPPGIATIVPGERLDERARPMIEYLQVFQEG 745

Query: 688 INLLPGFAPELQGVYIE-EHDGRKQVWCYVIKPRDAQS 724
            N  PGF  E+QG+Y E E DG  + + YV++   A +
Sbjct: 746 ANRFPGFDNEIQGLYRETEPDGSVRFYTYVVREDGADA 783


Lambda     K      H
   0.322    0.138    0.424 

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: 1537
Number of extensions: 68
Number of successful extensions: 5
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: 732
Length of database: 785
Length adjustment: 40
Effective length of query: 692
Effective length of database: 745
Effective search space:   515540
Effective search space used:   515540
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 (21.9 bits)
S2: 55 (25.8 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