GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagF in Pseudomonas putida KT2440

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>lcl|FitnessBrowser__Putida:PP_0793 PP_0793 Phosphotransferase
           system, fructose-specific EI/HPr/EIIA components
          Length = 950

 Score =  453 bits (1166), Expect = e-131
 Identities = 282/672 (41%), Positives = 389/672 (57%), Gaps = 19/672 (2%)

Query: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRK---AAIESVVGLLGLGAGEGATV 237
           +V L +  GLHARPA    + A+GF+  + VR         +++S+  LL LGA  G  +
Sbjct: 286 RVVLANPHGLHARPAKVLAQLAKGFEGEIRVRLVDSAQPAVSVKSLSKLLSLGARRGQAL 345

Query: 238 ELLGMGPQAAAAVAAIANELTREAHGEVEEKP---ARQSSPAPQAVARPAGETLAPNTLA 294
           EL+     AA A+  +   + +    EVE  P   A  +   P+ +  PA    A + + 
Sbjct: 346 ELVAEPSIAADALPVLLAAIEQGLGEEVEPLPQSVAPIADDVPEVLQAPA----AGSRIQ 401

Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354
           GV AAPG+A G      + + D P +   + A E + L +A+ATV+ +L   V  + +  
Sbjct: 402 GVGAAPGIASGPAHVCVEREFDYPLRGE-SCALERQKLREALATVNGELQALVLRSDK-- 458

Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414
           A+GE  IF  H+ +L DP L D     ++ G+SA  AW   I A       + DALLAER
Sbjct: 459 AIGE--IFVTHQEMLADPALTDDVEQRLAQGESAAAAWMAVIEAAARQQEALHDALLAER 516

Query: 415 AADLRDIEKRVLRALGYTSATARTLPEEA-VLAAEEFTPSDLSTLDRSRVTALVMARGGA 473
           AADLRDI +RVL  L      A+  PE+  VL   E  PSD++ LD +RV  +V A+GGA
Sbjct: 517 AADLRDIGRRVLAQL--CGVQAQVEPEQPYVLVMTEVGPSDVARLDPNRVAGIVTAQGGA 574

Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533
           T+H+AI+AR  GIPA+V  G ++  +  GT ++++   G +  AP   +++RA  ER   
Sbjct: 575 TAHSAIVARALGIPAVVGAGASILLLESGTPLLLDGQRGVVSVAPPADELQRALAERDLR 634

Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593
               +A      + A+T DG A+EV ANI   +     VE GA+ VGLLRTEL+F+    
Sbjct: 635 EQRLQAAWANRFEPAITRDGHAVEVFANIGDSNGIAKVVEQGAEGVGLLRTELIFMAHPQ 694

Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653
           AP        Y+ ++D L GR  ++RTLDVG DK + Y  +  E NP LG+RG+RL   R
Sbjct: 695 APDVATQEAEYRRVLDGLDGRPLVVRTLDVGGDKPLPYWPIAAEENPFLGVRGVRLTLQR 754

Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713
           P +++DQLR LL       +RI+ PMV  V E    R  ++    E+   + +++G+M+E
Sbjct: 755 PQVMEDQLRALLRAADQRPLRIMFPMVGQVHEWREARAMVERLRAEIPVAD-LQLGIMVE 813

Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773
           VPSAALLA QLA+  DF SIGTNDLTQYTLA+DR    L+AQADGLHPAVL LI  TV+ 
Sbjct: 814 VPSAALLAAQLAREVDFFSIGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLSLIDMTVRA 873

Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833
           A  HGKWVGVCG LA DP A+ +L+GL V ELSV   S+  +KA VR  D+Q  R  A++
Sbjct: 874 AHAHGKWVGVCGELAADPQAVAVLLGLDVDELSVSARSIAEVKALVRQADHQTARALARE 933

Query: 834 ALALESAQAVRA 845
           AL  +SA AVRA
Sbjct: 934 ALQQDSAAAVRA 945


Lambda     K      H
   0.317    0.133    0.371 

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: 1746
Number of extensions: 85
Number of successful extensions: 3
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: 854
Length of database: 950
Length adjustment: 43
Effective length of query: 811
Effective length of database: 907
Effective search space:   735577
Effective search space used:   735577
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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 preprint 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