Aligments for a candidate for nagF in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments 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)



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

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources