GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3291
          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:

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