Alignments for a candidate for fucK in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucK in Escherichia coli BW25113

Align L-fuculokinase; L-fuculose kinase; EC 2.7.1.51 (characterized)
to candidate 16887 b2803 L-fuculokinase (NCBI)

Query= SwissProt::P11553
         (472 letters)



>FitnessBrowser__Keio:16887
          Length = 482

 Score =  952 bits (2461), Expect = 0.0
 Identities = 472/472 (100%), Positives = 472/472 (100%)

Query: 1   MKQEVILVLDCGATNVRAIAVNRQGKIVARASTPNASDIAMENNTWHQWSLDAILQRFAD 60
           MKQEVILVLDCGATNVRAIAVNRQGKIVARASTPNASDIAMENNTWHQWSLDAILQRFAD
Sbjct: 11  MKQEVILVLDCGATNVRAIAVNRQGKIVARASTPNASDIAMENNTWHQWSLDAILQRFAD 70

Query: 61  CCRQINSELTECHIRGIAVTTFGVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISA 120
           CCRQINSELTECHIRGIAVTTFGVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISA
Sbjct: 71  CCRQINSELTECHIRGIAVTTFGVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISA 130

Query: 121 QRLQAISGVGAFSFNTLYKLVWLKENHPQLLERAHAWLFISSLINHRLTGEFTTDITMAG 180
           QRLQAISGVGAFSFNTLYKLVWLKENHPQLLERAHAWLFISSLINHRLTGEFTTDITMAG
Sbjct: 131 QRLQAISGVGAFSFNTLYKLVWLKENHPQLLERAHAWLFISSLINHRLTGEFTTDITMAG 190

Query: 181 TSQMLDIQQRDFSPQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVISAG 240
           TSQMLDIQQRDFSPQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVISAG
Sbjct: 191 TSQMLDIQQRDFSPQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVISAG 250

Query: 241 HDTQFALFGAGAEQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAGLYNPGM 300
           HDTQFALFGAGAEQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAGLYNPGM
Sbjct: 251 HDTQFALFGAGAEQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAGLYNPGM 310

Query: 301 QWLASGVLEWVRKLFWTAETPWQMLIEEARLIAPGADGVKMQCDLLSCQNAGWQGVTLNT 360
           QWLASGVLEWVRKLFWTAETPWQMLIEEARLIAPGADGVKMQCDLLSCQNAGWQGVTLNT
Sbjct: 311 QWLASGVLEWVRKLFWTAETPWQMLIEEARLIAPGADGVKMQCDLLSCQNAGWQGVTLNT 370

Query: 361 TRGHFYRAALEGLTAQLQRNLQMLEKIGHFKASELLLVGGGSRNTLWNQIKANMLDIPVK 420
           TRGHFYRAALEGLTAQLQRNLQMLEKIGHFKASELLLVGGGSRNTLWNQIKANMLDIPVK
Sbjct: 371 TRGHFYRAALEGLTAQLQRNLQMLEKIGHFKASELLLVGGGSRNTLWNQIKANMLDIPVK 430

Query: 421 VLDDAETTVAGAALFGWYGVGEFNSPEEARAQIHYQYRYFYPQTEPEFIEEV 472
           VLDDAETTVAGAALFGWYGVGEFNSPEEARAQIHYQYRYFYPQTEPEFIEEV
Sbjct: 431 VLDDAETTVAGAALFGWYGVGEFNSPEEARAQIHYQYRYFYPQTEPEFIEEV 482


Lambda     K      H
   0.320    0.134    0.410 

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: 970
Number of extensions: 24
Number of successful extensions: 1
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: 472
Length of database: 482
Length adjustment: 33
Effective length of query: 439
Effective length of database: 449
Effective search space:   197111
Effective search space used:   197111
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: 51 (24.3 bits)

Align candidate 16887 b2803 (L-fuculokinase (NCBI))
to HMM TIGR02628 (fucK: L-fuculokinase (EC 2.7.1.51))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02628.hmm
# target sequence database:        /tmp/gapView.1238.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02628  [M=465]
Accession:   TIGR02628
Description: fuculo_kin_coli: L-fuculokinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-259  846.5   0.6   3.4e-259  846.3   0.6    1.0  1  lcl|FitnessBrowser__Keio:16887  b2803 L-fuculokinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16887  b2803 L-fuculokinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  846.3   0.6  3.4e-259  3.4e-259       1     465 []      14     473 ..      14     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 846.3 bits;  conditional E-value: 3.4e-259
                       TIGR02628   1 evvlvldcGatnlraiainekGkivasasvknetkqaiensdyhiwdleeilqklvecaqkvqaevdekdilgiavttf 79 
                                     ev+lvldcGatn+raia+n++Gkiva+as++n++++a+en+++h+w+l++ilq++++c++++++e++e++i+giavttf
  lcl|FitnessBrowser__Keio:16887  14 EVILVLDCGATNVRAIAVNRQGKIVARASTPNASDIAMENNTWHQWSLDAILQRFADCCRQINSELTECHIRGIAVTTF 92 
                                     69***************************************************************************** PP

                       TIGR02628  80 GvdGapfdeqgnqlypiiswkcprtvpvmenvereldakrlyrrnGiGdysfntlyklrwlkehkpqllekmdkfvfis 158
                                     GvdGa++d+qgn+lypiiswkcprt++vm+n+er ++a+rl++++G+G++sfntlykl+wlke++pqlle++++++fis
  lcl|FitnessBrowser__Keio:16887  93 GVDGALVDKQGNLLYPIISWKCPRTAAVMDNIERLISAQRLQAISGVGAFSFNTLYKLVWLKENHPQLLERAHAWLFIS 171
                                     ******************************************************************************* PP

                       TIGR02628 159 slithrltGefttditmaGtsmmtdltsrnfdpailealGlseelfpplveaGekiGklrsdlakllGlnadvpvisaG 237
                                     sli+hrltGefttditmaGts+m+d+++r+f+p+il+a+G++++lfp+lveaGe+iG+l++++a++lGl++++pvisaG
  lcl|FitnessBrowser__Keio:16887 172 SLINHRLTGEFTTDITMAGTSQMLDIQQRDFSPQILQATGIPRRLFPRLVEAGEQIGTLQNSAAAMLGLPVGIPVISAG 250
                                     ******************************************************************************* PP

                       TIGR02628 238 hdtqfalfGsGaeenqpvlssGtweilmarsqraelslealsaGvtveldsqaglynpavqwlasgvvewvakllftae 316
                                     hdtqfalfG+Gae+n+pvlssGtweilm+rs+++++sl +++aG+t+eldsqaglynp++qwlasgv+ewv+kl++tae
  lcl|FitnessBrowser__Keio:16887 251 HDTQFALFGAGAEQNEPVLSSGTWEILMVRSAQVDTSLLSQYAGSTCELDSQAGLYNPGMQWLASGVLEWVRKLFWTAE 329
                                     ******************************************************************************* PP

                       TIGR02628 317 tasdelykvlieearkvangakgvvnletdlsslgqgaieGlslfttrGeiyraaleglakklkrrldvlekvsqlkak 395
                                     t+    +++lieear +a+ga+gv+ +++dl s+++++++G++l+ttrG++yraalegl+++l+r+l++lek++++ka+
  lcl|FitnessBrowser__Keio:16887 330 TP----WQMLIEEARLIAPGADGVK-MQCDLLSCQNAGWQGVTLNTTRGHFYRAALEGLTAQLQRNLQMLEKIGHFKAS 403
                                     **....*******************.***************************************************** PP

                       TIGR02628 396 elvvvGGGsknvlwnqiranaldlpvkvvddaeatvlGaalfafaGvGiyedveeaqaqlkpslrvvyps 465
                                     el++vGGGs+n+lwnqi+an+ld+pvkv+ddae+tv+Gaalf+++GvG+++++eea+aq+++++r++yp+
  lcl|FitnessBrowser__Keio:16887 404 ELLLVGGGSRNTLWNQIKANMLDIPVKVLDDAETTVAGAALFGWYGVGEFNSPEEARAQIHYQYRYFYPQ 473
                                     *********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (465 nodes)
Target sequences:                          1  (482 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.40
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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