GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Escherichia coli BW25113

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate 16488 b2383 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>lcl|FitnessBrowser__Keio:16488 b2383 fused predicted PTS enzymes:
           Hpr component/enzyme I component/enzyme IIA component
           (NCBI)
          Length = 831

 Score =  330 bits (846), Expect = 2e-94
 Identities = 227/677 (33%), Positives = 346/677 (51%), Gaps = 26/677 (3%)

Query: 177 PTGLHARPATAWVETARASAARIQ-VRHG-DLVADAKALVALLQLGLRAGDSVVVSAEGD 234
           P GLHARPA    E      + I  + H  +  ADAK+ +AL+  G    DS  ++  G 
Sbjct: 11  PNGLHARPAWELKEQCSQWQSEITFINHRQNAKADAKSSLALIGTGTLFNDSCSLNISGS 70

Query: 235 DAVAALARMKATI-TRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIG 293
           D   A   ++  I  R    +      A   A    R  +  NP      + AS G+ +G
Sbjct: 71  DEEQARRVLEEYIQVRFIDSDSVQPTQAELTAHPLPRSLSRLNPDLLYGNVLAS-GVGVG 129

Query: 294 PVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQA 353
            + +L   ++          +   RL  +L+   + L         R G S+  I +A  
Sbjct: 130 TLTLLQSDSLDSYRAIPASAQDSTRLEHSLATLAEQLN---QQLRERDGESKT-ILSAHL 185

Query: 354 EILNDTDLVTLACQLMVEGH-GVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRV 412
            ++ D +      +LM E H G+  +    +E+  A L+A  +  L  R +D+RD+ +++
Sbjct: 186 SLIQDDEFAGNIRRLMTEQHQGLGAAIISNMEQVCAKLSASASDYLRERVSDIRDISEQL 245

Query: 413 LARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILAR 472
           L    P L+      L + P IL+AEDL+PS   +LD+  + G+   + G TSHT ILAR
Sbjct: 246 LHITWPELKPRNKLVL-EKPTILVAEDLTPSQFLSLDLKNLAGMILEKTGRTSHTLILAR 304

Query: 473 TLGLPAMVAGGAALMELAN--GTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEE 530
              +P  V  G  L  +A   G PA+LD Q G L ++P  A     +      + R+ ++
Sbjct: 305 ASAIP--VLSGLPLDAIARYAGQPAVLDAQCGVLAINPNDAVSGYYQVAQTLADKRQKQQ 362

Query: 531 EARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQ 590
                  A +RD   ++I AN+    +   A + GAE VGL RTE L+++R  AP E EQ
Sbjct: 363 AQAAAQLAYSRDNKRIDIAANIGTALEAPGAFANGAEGVGLFRTEMLYMDRDSAPDEQEQ 422

Query: 591 YETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQ 650
           +E Y+ +L A   +P+I R +DIGGDK +P+L +P EENPFLG R  R+      L  TQ
Sbjct: 423 FEAYQQVLLAAGDKPIIFRTMDIGGDKSIPYLNIPQEENPFLGYRAVRIYPEFAGLFRTQ 482

Query: 651 LRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAELD------APAVPLG 704
           LRA+ RAA  G A+      +M PM+ +L ++  ++   ++   EL       A  + LG
Sbjct: 483 LRAILRAASFGNAQ------LMIPMVHSLDQILWVKGEIQKAIVELKRDGLRHAETITLG 536

Query: 705 IMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRL 764
           IMVEVP+     D     VDFFSIG+ND+TQY  A+DR +P ++   + + P+ LR+++ 
Sbjct: 537 IMVEVPSVCYIIDHFCDEVDFFSIGSNDMTQYLYAVDRNNPRVSPLYNPITPSFLRMLQQ 596

Query: 765 TVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKD 824
            V  A + G+WVG+CG + G+     LL GLG+ ELSM+   IPAVK +LR  D  A ++
Sbjct: 597 IVTTAHQRGKWVGICGELGGESRYLPLLLGLGLDELSMSSPRIPAVKSQLRQLDSEACRE 656

Query: 825 AAQRALDCETADAVRAL 841
            A++A +C +A  + AL
Sbjct: 657 LARQACECRSAQEIEAL 673



 Score = 38.9 bits (89), Expect = 1e-06
 Identities = 38/154 (24%), Positives = 68/154 (44%), Gaps = 13/154 (8%)

Query: 7   TAIMPTDLLRP----ELLRLSASPAGKEEAIREAAQLLIAAGCIDSAYAAS--MLRREAV 60
           TA  P + +RP    E + +    + KE+AI+     L   G  +  +     + +RE +
Sbjct: 675 TAFTPEEDVRPLLALENIFVDQDFSNKEQAIQFLCGNLGVNGRTEHPFELEEDVWQREEI 734

Query: 61  ANTFLGHGVAIPHGMVEDRGMVRRSGIAVLQVPGGIAWNPGQ-TAHLVVAI---AAQSDA 116
             T +G GVAIPH   +    +R S I++ ++   I W        LV+ +   A +   
Sbjct: 735 VTTGVGFGVAIPHTKSQ---WIRHSSISIARLAKPIGWQSEMGEVELVIMLTLGANEGMN 791

Query: 117 HIAVLRRLTRLMQDEARLTALFTVTDPAALAAAL 150
           H+ V  +L R + ++    +LF   D  ++   L
Sbjct: 792 HVKVFSQLARKLVNKNFRQSLFAAQDAQSILTLL 825


Lambda     K      H
   0.319    0.134    0.387 

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: 1196
Number of extensions: 33
Number of successful extensions: 6
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: 846
Length of database: 831
Length adjustment: 42
Effective length of query: 804
Effective length of database: 789
Effective search space:   634356
Effective search space used:   634356
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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