GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_0793
          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:

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