GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Pseudomonas putida KT2440

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate PP_2329 PP_2329 aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex

Query= curated2:P05378
         (462 letters)



>FitnessBrowser__Putida:PP_2329
          Length = 446

 Score =  249 bits (637), Expect = 1e-70
 Identities = 165/454 (36%), Positives = 235/454 (51%), Gaps = 44/454 (9%)

Query: 21  AYLKLAEKAPVSFLLESVERGRQ-SRFSIVGVGARRTFRLKDGVFTVNGERVETRDPLRA 79
           AY     +AP + LL+S   G +  RF ++              + +   + +  +  R 
Sbjct: 17  AYFAHLRQAPGAILLDSARPGAERGRFDLLSA------------WPLQQLQAQPDEDGRV 64

Query: 80  LYERVYAPLER--HPDLP-----PFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDLLFV 132
             +R+ A L +  H DLP     PF GG++GY +YD  R  E LPSL  DDLGLPD    
Sbjct: 65  FLQRLRAGLAQLGHADLPNGVELPFAGGLIGYLSYDFGRRLEHLPSLAVDDLGLPDAQLG 124

Query: 133 EPEVVAVFDHLKNLLHLV---APGRDPEEAEARLFW------AERRLKGPLPGVPGERAG 183
                 V DHL     LV   +   D  E    LF        + RL  P+ G       
Sbjct: 125 LYAWALVSDHLLGTSQLVFHPSLAGDERERLISLFQDTSATTGDFRLLAPMAG------- 177

Query: 184 GRARFQADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPS 243
                  D   E Y  A  +   YI+AGD +Q+ L+ R  +P    P+  Y+ALR   P+
Sbjct: 178 -------DLEPEQYKTAFDQVQRYIQAGDCYQINLTQRFRAPCQGDPWRAYQALRQACPT 230

Query: 244 PYMGYLDLGE-VVLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEK 302
           P+ GY  L +   L+S SPE  +R    +V TRPI GTRPR  D  +D+R A+ELL   K
Sbjct: 231 PFSGYQQLADGSTLLSFSPERFIRVSQGQVETRPIKGTRPRASDPAQDQRNAQELLHSPK 290

Query: 303 EVAEHVMLLDLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDAL 362
           + +E++M++DL RND+GR    G+V+V E   +E Y +V HLVS++ G LA  K  LD +
Sbjct: 291 DRSENLMIVDLLRNDLGRTCEIGSVKVPELFSLESYPNVHHLVSSITGQLASDKDALDLI 350

Query: 363 ASVLPMGTVSGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGW 422
               P G+++GAPKIRAM+II+ELEP RR  Y GS  Y+   G MD ++ +R+ ++  G 
Sbjct: 351 GDSFPGGSITGAPKIRAMQIIDELEPARRALYCGSLLYVDVRGEMDSSIAIRSLLIKDGQ 410

Query: 423 MHVQAGAGIVADSVPEREYEECWNKARALLKAVE 456
           +    G  +VADS  + EYEE   K R L++ ++
Sbjct: 411 VSCWGGGAVVADSQWQAEYEESIAKVRVLMQTLQ 444


Lambda     K      H
   0.321    0.139    0.408 

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: 515
Number of extensions: 31
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: 462
Length of database: 446
Length adjustment: 33
Effective length of query: 429
Effective length of database: 413
Effective search space:   177177
Effective search space used:   177177
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 Aug 03 2021. The underlying query database was built on Aug 03 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