GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagF in Pseudomonas stutzeri RCH2

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase

Query= TCDB::Q9HXN5
         (842 letters)



>lcl|FitnessBrowser__psRCH2:GFF3291 Psest_3355
           phosphoenolpyruvate-protein phosphotransferase
          Length = 960

 Score =  455 bits (1171), Expect = e-132
 Identities = 272/678 (40%), Positives = 383/678 (56%), Gaps = 26/678 (3%)

Query: 180 VAHHGGLHARPAALLRKTAQGFSSQAELHFAGQVA---SVDSLVGIMGLGVAEQDEVEVI 236
           +A+  GLHARPA +L + AQ F  +  +  AG  +   SV SL  ++ +G      +E +
Sbjct: 289 LANAHGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFM 348

Query: 237 CRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLA------------ 284
                +  AL AL+ A+        +  P   APGE + P   A   A            
Sbjct: 349 AEPAIASDALPALVRAVEEGLGEEVEPLP---APGEASEPPVTAQGPAESAIDQAALRAG 405

Query: 285 ----GVCASPGLASGPLARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQAR 340
               G+ ASPG+A GP+       +        P  +   LD AL +V  D+   + +++
Sbjct: 406 DQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQ 465

Query: 341 LGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLL 400
           +    +   IF+ H A+L+DP L +   + + +G+ A  AW   I++  +  +AL + LL
Sbjct: 466 VASIRD---IFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLL 522

Query: 401 AERANDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGG 460
           AERA DLRD+ +RVL  L G  A        I+   E+ PSD+A L     AG+  A GG
Sbjct: 523 AERAADLRDVGRRVLACLTGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGG 582

Query: 461 ATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQ 520
           ATSH AI+AR+ G+P +V  G G+L L     ++LD  +G L ++P   +LEQ   + A 
Sbjct: 583 ATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAA 642

Query: 521 REEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERR 580
           REE++          A+TRDG  +EI AN+ +  E  EA A GA+G+GLLRTE +F+   
Sbjct: 643 REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHS 702

Query: 581 AAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQA 640
            AP++  Q   Y+ VL+A+  R +++RT+DVGGDK L Y P+P EENP LG+RGI L   
Sbjct: 703 QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQ 762

Query: 641 RPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMI 700
           RP++L+ QLRALL        RI+ PMV  +DE R  +  +  L  +L +  L ++G+MI
Sbjct: 763 RPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADL-QVGIMI 821

Query: 701 EVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCA 760
           E+PSAAL+A  LA+  DF SIGTNDL+QY LA+DR H  L+ + D LHPA+LRLI  T  
Sbjct: 822 EIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVE 881

Query: 761 GAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQ 820
            A  HG+WVGVCG LA+D LA P+LVGLGV+ELSV    +  +K RVR+LD A C+R AQ
Sbjct: 882 AAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQ 941

Query: 821 ALLDLGSARAVRDACLQH 838
             L L  A  VR    +H
Sbjct: 942 QALMLPGAHEVRAFVGEH 959


Lambda     K      H
   0.319    0.136    0.390 

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: 2036
Number of extensions: 115
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: 842
Length of database: 960
Length adjustment: 43
Effective length of query: 799
Effective length of database: 917
Effective search space:   732683
Effective search space used:   732683
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 (21.7 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