GapMind for catabolism of small carbon sources

 

Alignments 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:

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