GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N1B4

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Pf1N1B4_1146 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1146
          Length = 953

 Score =  455 bits (1170), Expect = e-132
 Identities = 285/672 (42%), Positives = 393/672 (58%), Gaps = 16/672 (2%)

Query: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRY-EGRKAAI--ESVVGLLGLGAGEGATV 237
           ++ L +  GLHARPA    + A+ F+  + VR  +G  +A+  +S+  LL LGA  G  +
Sbjct: 286 RIALANTHGLHARPAKILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVL 345

Query: 238 ELLGMGPQAAAAVAAIANELTREAHGEVEEKPARQSSPAPQAVARPAGETLAP---NTLA 294
           E +     AA A+ A+   +      EVE  PA   S   + +A  A   LAP   + + 
Sbjct: 346 EFIAEPTIAADALPALLAAIEEGLGEEVEPLPA--VSQHREVIADVAEVLLAPASGSLIQ 403

Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354
            + AAPG+A+G         ID P +   ++A E   L +A+A V  D++  + + S+  
Sbjct: 404 AIAAAPGIAIGPAHIQVQQVIDYPLRGE-SAAIERERLKQALADVRRDIEGLI-ERSKAK 461

Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414
           A+ E  IF  H+ +L+DP L D     +  G+SA  AW   I A      +++DALLAER
Sbjct: 462 AIRE--IFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAER 519

Query: 415 AADLRDIEKRVLRALGYTSATARTLPEEA-VLAAEEFTPSDLSTLDRSRVTALVMARGGA 473
           AADLRDI +RVL  L      A   PE+  +L  +E  PSD++ LD +RV  ++ ARGGA
Sbjct: 520 AADLRDIGRRVLAQLSGVETPAE--PEQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 577

Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533
           T+H+AI+AR  GIPALV  G A+  +  GT ++++   GRL        ++RA  ER   
Sbjct: 578 TAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTR 637

Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593
               +A      Q A+T+DG A+EV ANI       +AVE GA+ +GLLRTEL+F+  + 
Sbjct: 638 ELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQ 697

Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653
           AP        Y+ ++D L+GR  ++RTLDVG DK + Y  +  E NP LG+RGIRL   R
Sbjct: 698 APDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQR 757

Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713
           P +++ QLR LL       +RI+ PMV  V E  + R   +    E+   + +++G+MIE
Sbjct: 758 PQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVAD-LQLGIMIE 816

Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773
           VPSAALLA  LA+  DF S+GTNDLTQYTLA+DR    L+AQADGLHPAVL+LI  TV+ 
Sbjct: 817 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 876

Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833
           A  HGKWVGVCG LA DPLA+P+LVGLGV ELSV   S+  +KAR+R L     +  AQ 
Sbjct: 877 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQ 936

Query: 834 ALALESAQAVRA 845
           ALA+ SA  VRA
Sbjct: 937 ALAVGSANEVRA 948


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: 1736
Number of extensions: 82
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: 953
Length adjustment: 43
Effective length of query: 811
Effective length of database: 910
Effective search space:   738010
Effective search space used:   738010
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