Alignments for a candidate for nagF in Escherichia coli BW25113

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 16488 b2383 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>FitnessBrowser__Keio:16488
          Length = 831

 Score =  343 bits (879), Expect = 3e-98
 Identities = 215/659 (32%), Positives = 342/659 (51%), Gaps = 22/659 (3%)

Query: 183 GLHARPAALVRQTAQGFKSRSQL--HFSGKSASCDSVMGMMGLAITEQAQVHVSCRGSDA 240
           GLHARPA  +++    ++S      H     A   S + ++G          ++  GSD 
Sbjct: 13  GLHARPAWELKEQCSQWQSEITFINHRQNAKADAKSSLALIGTGTLFNDSCSLNISGSDE 72

Query: 241 EAALQALLTTLSTALVE-------EAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLV 293
           E A + L   +    ++       +A  +A P     +     +L+G   A G+  G L 
Sbjct: 73  EQARRVLEEYIQVRFIDSDSVQPTQAELTAHPLPRSLSRLNPDLLYGNVLASGVGVGTLT 132

Query: 294 RLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALL 353
            L    L       A  +   RL  +LA +  +++  L      +  + + I SAHL+L+
Sbjct: 133 LLQSDSLDSYRAIPASAQDSTRLEHSLATLAEQLNQQLRE----RDGESKTILSAHLSLI 188

Query: 354 EDPVLL-DAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRV 412
           +D     +   L  EQ      A   +++  C  L    S  L ER +D+RD+ +++L +
Sbjct: 189 QDDEFAGNIRRLMTEQHQGLGAAIISNMEQVCAKLSASASDYLRERVSDIRDISEQLLHI 248

Query: 413 LLGEAW---QFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGL 469
              E     +  +    I+ A++LTPS  L L  + +AG+ + + G TSH  ILAR   +
Sbjct: 249 TWPELKPRNKLVLEKPTILVAEDLTPSQFLSLDLKNLAGMILEKTGRTSHTLILARASAI 308

Query: 470 PCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHT 529
           P L  L  + +A+  GQ  VLDA  G L + P        + AQT     + QQ   A  
Sbjct: 309 PVLSGLPLDAIARYAGQPAVLDAQCGVLAINPNDAVSGYYQVAQTLADKRQKQQAQAAAQ 368

Query: 530 PARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTAPDEEEQRQAYQA 589
            A + D   +++AAN+ ++ EA  + ANGA+GVGL RTE L++DR +APDE+EQ +AYQ 
Sbjct: 369 LAYSRDNKRIDIAANIGTALEAPGAFANGAEGVGLFRTEMLYMDRDSAPDEQEQFEAYQQ 428

Query: 590 VLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRPDLLDQQLRALLQ 649
           VL A GDKP+I RT+D+GGDK + YL +P E NP LG R +R+      L   QLRA+L+
Sbjct: 429 VLLAAGDKPIIFRTMDIGGDKSIPYLNIPQEENPFLGYRAVRIYPEFAGLFRTQLRAILR 488

Query: 650 TRPLDRCRILLPMVTEVDELLHIRKRLDALGSEL---GL--SERPQLGVMVEVPAAALLA 704
                  ++++PMV  +D++L ++  +     EL   GL  +E   LG+MVEVP+   + 
Sbjct: 489 AASFGNAQLMIPMVHSLDQILWVKGEIQKAIVELKRDGLRHAETITLGIMVEVPSVCYII 548

Query: 705 EQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWV 764
           +   +  DF SIG+ND++QY  A+DR++  ++   + + P+ LR++ Q    A + G+WV
Sbjct: 549 DHFCDEVDFFSIGSNDMTQYLYAVDRNNPRVSPLYNPITPSFLRMLQQIVTTAHQRGKWV 608

Query: 765 GVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLSNELLNLGSA 823
           G+CG L  +    P+L+GLG+ ELS+S P+I  +K ++R LD+  C  L+ +     SA
Sbjct: 609 GICGELGGESRYLPLLLGLGLDELSMSSPRIPAVKSQLRQLDSEACRELARQACECRSA 667


Lambda     K      H
   0.319    0.134    0.386 

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: 1234
Number of extensions: 50
Number of successful extensions: 3
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: 837
Length of database: 831
Length adjustment: 42
Effective length of query: 795
Effective length of database: 789
Effective search space:   627255
Effective search space used:   627255
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 (21.8 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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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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