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 16515 b2416 PEP-protein phosphotransferase of PTS system (enzyme I) (NCBI)

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



>lcl|FitnessBrowser__Keio:16515 b2416 PEP-protein phosphotransferase
           of PTS system (enzyme I) (NCBI)
          Length = 575

 Score =  389 bits (998), Expect = e-112
 Identities = 232/567 (40%), Positives = 339/567 (59%), Gaps = 17/567 (2%)

Query: 408 VNGIAASPGIAIGPVLVRKPQ--VIDYPKRGESPVI-ELQRLDAALDKVHADIGTL---I 461
           ++GI ASPGIA G  L+ K    VID  K     V  E++R  +   K  A + T+    
Sbjct: 2   ISGILASPGIAFGKALLLKEDEIVIDRKKISADQVDQEVERFLSGRAKASAQLETIKTKA 61

Query: 462 DESQVASIRDIFTTHQAMLKDPALREEVQVRLQ-KGLSAEAAWMEEIESAAQQQEALHDK 520
            E+       IF  H  +L+D  L +E+   ++ K ++A+AA  E IE  A   E L D+
Sbjct: 62  GETFGEEKEAIFEGHIMLLEDEELEQEIIALIKDKHMTADAAAHEVIEGQASALEELDDE 121

Query: 521 LLAERAADLRDVGRRVLACLTGVEAEQ--APDEPYILVMDEVAPSDVATLNAQRVAGILT 578
            L ERAAD+RD+G+R+L  + G++     A  +  ILV  ++ PS+ A LN ++V G +T
Sbjct: 122 YLKERAADVRDIGKRLLRNILGLKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFIT 181

Query: 579 AGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARS 638
             GG TSH++I+AR+L +PAIVG G     +  +  L+LD    ++ V P+   +++ R+
Sbjct: 182 DAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRA 241

Query: 639 -ERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELV 697
            +     E+  LA  + + A +T DGH VE+ ANIG   +   A   GAEG+GL RTE +
Sbjct: 242 VQEQVASEKAELAKLKDLPA-ITLDGHQVEVCANIGTVRDVEGAERNGAEGVGLYRTEFL 300

Query: 698 FMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGI 757
           FM+    P +  Q A Y+ V EA   + ++VRT+D+GGDK LPY   P EENPFLG R I
Sbjct: 301 FMDRDALPTEEEQFAAYKAVAEACGSQAVIVRTMDIGGDKELPYMNFPKEENPFLGWRAI 360

Query: 758 RLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVA---- 813
           R+++ R +IL  QLRA+L ++    LRIMFPM+ +++E R  +  ++  + EL       
Sbjct: 361 RIAMDRREILRDQLRAILRASAFGKLRIMFPMIISVEEVRALRKEIEIYKQELRDEGKAF 420

Query: 814 --DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPA 871
              +++G+M+E P+AA IA  LA+EVDFFSIGTNDLTQYTLA+DRG+  +S     + P+
Sbjct: 421 DESIEIGVMVETPAAATIARHLAKEVDFFSIGTNDLTQYTLAVDRGNDMISHLYQPMSPS 480

Query: 872 VLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVREL 931
           VL LI   ++A+HA GKW G+CGELA D  A  LL+G+G+DE S+SA SI  +K  +R  
Sbjct: 481 VLNLIKQVIDASHAEGKWTGMCGELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNT 540

Query: 932 DFAACQRLAQQALMLPGAHEVRAFVGE 958
           +F   + LA+QAL  P   E+   V +
Sbjct: 541 NFEDAKVLAEQALAQPTTDELMTLVNK 567


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: 989
Number of extensions: 38
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: 960
Length of database: 575
Length adjustment: 40
Effective length of query: 920
Effective length of database: 535
Effective search space:   492200
Effective search space used:   492200
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: 55 (25.8 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