GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Escherichia coli BW25113

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)

Query= reanno::psRCH2:GFF3291
         (960 letters)



>FitnessBrowser__Keio:1937187
          Length = 833

 Score =  333 bits (854), Expect = 3e-95
 Identities = 223/691 (32%), Positives = 354/691 (51%), Gaps = 49/691 (7%)

Query: 293 HGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLS------------KLLAMGAH 340
           +G+HARPA  +  +   F  +I      T+  G +  +L+            +LL  GA 
Sbjct: 13  NGVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGAD 72

Query: 341 RGQLLEFMAEPAIASDALPALVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQA 400
             +  + +++     D  P     + E   +E+EPLP       P +             
Sbjct: 73  EQEAHQRLSQ--WLRDEFPHCDAPLAEVKSDELEPLPVSLTNLNPQI------------- 117

Query: 401 ALRAGDQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTL 460
            +RA    +G   S G  + P+       +      +    E   L+  L  V  +I   
Sbjct: 118 -IRARTVCSG---SAGGILTPISSLDLNALGNLPAAKGVDAEQSALENGLTLVLKNIEFR 173

Query: 461 IDESQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDK 520
           + +S  A+   I   H+++  D +LRE +   +  GLS   A +       ++       
Sbjct: 174 LLDSDGATSA-ILEAHRSLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSS 232

Query: 521 LLAERAADLRDVGRRVLACLTGVEAEQAPD---EPYILVMDEVAPSDVATLNAQRVAGIL 577
            L ERA D+RDV  ++L  + G +   AP    +P I + DE+ PS    L+   + G+L
Sbjct: 233 YLQERALDVRDVCFQLLQQIYGEQRFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLL 292

Query: 578 TAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQL---- 633
              GG TSH+ I+AR+  IP +VG     L   +   + +DG  G ++V P  A      
Sbjct: 293 LKSGGTTSHTVILARSFNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAVARYYQ 352

Query: 634 EQARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLR 693
           ++AR + A RE+++    ++    A T DG  +EIAANI  + E   A   GAEG+GL R
Sbjct: 353 QEARVQDALREQQRVWLTQQ----ARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFR 408

Query: 694 TELVFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLG 753
           TE+++M+ + AP ++     + + LE+  GR ++VRT+D+GGDKP+ Y  +PAE NPFLG
Sbjct: 409 TEMLYMDRTSAPGESELYNIFCQALESANGRSIIVRTMDIGGDKPVDYLNIPAEANPFLG 468

Query: 754 VRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDE--W---RTAKAMVDRLRV 808
            R +R+  +   +  TQLR++L ++    L+IM PM+ +++E  W   + A+A       
Sbjct: 469 YRAVRIYEEYASLFTTQLRSILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNE 528

Query: 809 ELPVAD-LQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADG 867
            +P  + +Q+GIM+E+PS   I     +E+DFFSIG+NDLTQY LA+DR +  ++   + 
Sbjct: 529 HIPFDEKIQLGIMLEVPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNS 588

Query: 868 LHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKAR 927
           L+PA LR +   V+A H  GKW+G+CGEL A    +PLLVGLG+DELS+SA SI   KAR
Sbjct: 589 LNPAFLRALDYAVQAVHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKAR 648

Query: 928 VRELDFAACQRLAQQALMLPGAHEVRAFVGE 958
           + +LD   C++L  QA+    + EV   + +
Sbjct: 649 MAQLDSRECRKLLNQAMACRTSLEVEHLLAQ 679



 Score = 50.1 bits (118), Expect = 6e-10
 Identities = 36/101 (35%), Positives = 49/101 (48%), Gaps = 6/101 (5%)

Query: 43  LRAREAQGSTFLGQGIAIPHGTPETRDQVFTTGVRLLHFPAGVDWGNGQ---LVYLAIGI 99
           L AREA  ST LG   AIPH   E  +Q   +  RL    A V WG+ +   ++ L +  
Sbjct: 731 LWAREAVFSTGLGFSFAIPHSKSEHIEQSTISVARL---QAPVRWGDDEAQFIIMLTLNK 787

Query: 100 AARSDEHLRLLQLLTRALGEGDLSEGLQQAESPEAIIGLLQ 140
            A  D+H+R+   L R +   +    L  A S +AI  LLQ
Sbjct: 788 HAAGDQHMRIFSRLARRIMHEEFRNALVNAASADAIASLLQ 828


Lambda     K      H
   0.317    0.134    0.384 

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: 1463
Number of extensions: 63
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 960
Length of database: 833
Length adjustment: 43
Effective length of query: 917
Effective length of database: 790
Effective search space:   724430
Effective search space used:   724430
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