GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:1937187 b3947 fused predicted PTS enzymes:
           Hpr component/enzyme I component/enzyme IIA component
           (NCBI)
          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 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