GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagF in Escherichia coli BW25113

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>FitnessBrowser__Keio:1937187
          Length = 833

 Score =  348 bits (894), Expect = e-100
 Identities = 214/671 (31%), Positives = 343/671 (51%), Gaps = 25/671 (3%)

Query: 183 GLHARPAALIRQTAHLFNSKSQLHF--AGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA 240
           G+HARPA+ +    + F+S+ + H     +  +  S + L+G      D  Q+   GAD 
Sbjct: 14  GVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGADE 73

Query: 241 KAALQALLNALSTAVNDDSHAAAPT---------PIAQRTRTAEAGVLNGVCAAPGLVGG 291
           + A Q L   L    ++  H  AP          P+          ++       G  GG
Sbjct: 74  QEAHQRLSQWLR---DEFPHCDAPLAEVKSDELEPLPVSLTNLNPQIIRARTVCSGSAGG 130

Query: 292 PLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHL 351
            L  ++++ L    G   A + + A   ALE   + + + +             I  AH 
Sbjct: 131 ILTPISSLDL-NALGNLPAAKGVDAEQSALENGLTLVLKNIEFRLLDSDGATSAILEAHR 189

Query: 352 ALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVL 411
           +L  D +L E  +  +  G +   A   S    CE   +  +  L ERA D+RD+  ++L
Sbjct: 190 SLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSSYLQERALDVRDVCFQLL 249

Query: 412 RALLGQDWHYDVPAG----AIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARG 467
           + + G+   +  P      AI  A ELTPS  L+L +  + GL +  GG TSH  ILAR 
Sbjct: 250 QQIYGEQ-RFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLLLKSGGTTSHTVILARS 308

Query: 468 KGLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQ 527
             +P LV +    L   Q Q++ +D + G + + P         Q  R     RE+Q+  
Sbjct: 309 FNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAVARYYQQEARVQDALREQQRVW 368

Query: 528 AHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQA 587
               A T DG+RIE+AAN+A S EA  A   GA+GVGL RTE L++DR +AP E E    
Sbjct: 369 LTQQARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFRTEMLYMDRTSAPGESELYNI 428

Query: 588 YQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRA 647
           +   L++   +S+I+RT+D+GGDK +DYL +PAEANP LG R +R+ +    L   QLR+
Sbjct: 429 FCQALESANGRSIIVRTMDIGGDKPVDYLNIPAEANPFLGYRAVRIYEEYASLFTTQLRS 488

Query: 648 LLQVSPLQRCRILLPMVTEVDELLYIRQRLDALCAEL-----ALTQRLELGVMIEVPAAA 702
           +L+ S     +I++PM++ ++E+L+++++L     +L        ++++LG+M+EVP+  
Sbjct: 489 ILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNEHIPFDEKIQLGIMLEVPSVM 548

Query: 703 LLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQ 762
            + +Q  E  DF SIG+NDL+QY LA+DRD+A +    ++L+PA LR +        +  
Sbjct: 549 FIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAVQAVHRQG 608

Query: 763 RWVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLS 822
           +W+G+CG L +     P+L+GLG+ ELS+S P +   K R+ QLD+ +CR+     +   
Sbjct: 609 KWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKARMAQLDSRECRKLLNQAMACR 668

Query: 823 SATAVRHACHQ 833
           ++  V H   Q
Sbjct: 669 TSLEVEHLLAQ 679


Lambda     K      H
   0.318    0.133    0.379 

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: 1342
Number of extensions: 58
Number of successful extensions: 4
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: 838
Length of database: 833
Length adjustment: 42
Effective length of query: 796
Effective length of database: 791
Effective search space:   629636
Effective search space used:   629636
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