GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas fluorescens GW456-L13

Align ornithine δ-aminotransferase (EC 2.6.1.13) (characterized)
to candidate PfGW456L13_1158 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= metacyc::MONOMER-16810
         (468 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1158
          Length = 427

 Score =  212 bits (539), Expect = 2e-59
 Identities = 139/391 (35%), Positives = 200/391 (51%), Gaps = 15/391 (3%)

Query: 39  IEYESDYSAHNYHPIPMVFSKAKDVHVWDPEGRKYLDFLSAYSAVNQGHCHEKILNALSQ 98
           +   S+Y   +      VF + +   +WD + R YLDF     A + GH    ++NA++ 
Sbjct: 27  VNLSSEYLMPSVERPKQVFVRGQGSWLWDSDDRAYLDFSQGGGANSLGHSPSVLVNAITA 86

Query: 99  QAQQLTLSSRAFHNDIFPIFAQHLTSMFGYEMILPMNTGAEGVETALKLARKWGYEKKHI 158
           QAQ L       HN      A+HL +  G +    +NTG+E  E A+KLARKWG  ++H 
Sbjct: 87  QAQSLINPGFGLHNRGMLSLAEHLCASTGSDQAYLLNTGSEACEAAIKLARKWG--QRHR 144

Query: 159 PKNEAIIISCCGCFHGRTTAVISMSCDNEATRGFGPFLPGLLKVDFGDADSLKSMFEAHG 218
                II++  GC HGR+ A IS S  +     F P LPG  +V F D   L ++  A  
Sbjct: 145 GGASRIIVANNGC-HGRSLATISASDSSTLANRFEPQLPGFSRVPFND---LPALHAAVD 200

Query: 219 DKVAGFLFEPIQGEAGVIVPPKGYLQSVRELCSKYNVLMIADEIQTGIGRTGKLLACEWE 278
           ++    + EPIQ EAGV+     YL+ V  LC +  +L+I DE+QTGIGR G LLA +  
Sbjct: 201 ERTVAIMLEPIQSEAGVVPATVHYLKGVERLCRELGILLIFDEVQTGIGRCGSLLAEQSC 260

Query: 279 SVRPDVVILGKALGGGVLPVSAVLADKDIMLCFKPGEHGSTFGGNPLASAVAIAALEIVE 338
            V  D+V+LGK LGGGV P++A+LA +    CF  GE   T  GN L +A  ++ L+ V+
Sbjct: 261 GVTADIVVLGKGLGGGV-PLAALLA-RGKACCFDIGELAGTHHGNALMTAAGLSVLDTVQ 318

Query: 339 EEKLAERAAEMGQVFRSQFLDIQKAYPHIIKEVRGQGLLNAVELNAKGLSTVSAFDICQR 398
           ++   +  AE GQ  R     +   Y H   E+RGQGLL  +      LS  SA  + + 
Sbjct: 319 DKAFLKHVAEAGQHLREGLGRLAHRYGH--GELRGQGLLWGLT-----LSDDSADAVVKA 371

Query: 399 LKERGVLAKPTHGTIIRFSPPLTIRLKELTE 429
               G+L        +RF+P L +    + E
Sbjct: 372 ALYEGLLLNAPQADCLRFTPALNVSNANIDE 402


Lambda     K      H
   0.319    0.136    0.405 

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: 460
Number of extensions: 23
Number of successful extensions: 4
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: 468
Length of database: 427
Length adjustment: 33
Effective length of query: 435
Effective length of database: 394
Effective search space:   171390
Effective search space used:   171390
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 (21.8 bits)
S2: 51 (24.3 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