Alignments for a candidate for fucK in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucK in Klebsiella michiganensis M5al

Align L-fuculokinase (EC 2.7.1.51) (characterized)
to candidate BWI76_RS22930 BWI76_RS22930 L-fuculokinase

Query= reanno::Koxy:BWI76_RS22930
         (472 letters)



>FitnessBrowser__Koxy:BWI76_RS22930
          Length = 472

 Score =  949 bits (2453), Expect = 0.0
 Identities = 472/472 (100%), Positives = 472/472 (100%)

Query: 1   MKKDVILVLDCGATNVRAIAVDRRGNIIARAATTNASDIAVENSAWHQWSLEAILQRFAE 60
           MKKDVILVLDCGATNVRAIAVDRRGNIIARAATTNASDIAVENSAWHQWSLEAILQRFAE
Sbjct: 1   MKKDVILVLDCGATNVRAIAVDRRGNIIARAATTNASDIAVENSAWHQWSLEAILQRFAE 60

Query: 61  CCRQISDPLSSCTVRGITVTTFGVDGALVDEQGKLLYPVISWKCPRTAAVMDNISRFMPA 120
           CCRQISDPLSSCTVRGITVTTFGVDGALVDEQGKLLYPVISWKCPRTAAVMDNISRFMPA
Sbjct: 61  CCRQISDPLSSCTVRGITVTTFGVDGALVDEQGKLLYPVISWKCPRTAAVMDNISRFMPA 120

Query: 121 QQLQQISGVGAFAFNTLYKLIWLKENHPQLLEKARAWLFISSLLNQRLTGEFTTDITMAG 180
           QQLQQISGVGAFAFNTLYKLIWLKENHPQLLEKARAWLFISSLLNQRLTGEFTTDITMAG
Sbjct: 121 QQLQQISGVGAFAFNTLYKLIWLKENHPQLLEKARAWLFISSLLNQRLTGEFTTDITMAG 180

Query: 181 TSQMLDIHQRDFSTQILQATGLPRRLFPRLVEAGQQIGTLQSDAAKMLGLAVGIPVISAG 240
           TSQMLDIHQRDFSTQILQATGLPRRLFPRLVEAGQQIGTLQSDAAKMLGLAVGIPVISAG
Sbjct: 181 TSQMLDIHQRDFSTQILQATGLPRRLFPRLVEAGQQIGTLQSDAAKMLGLAVGIPVISAG 240

Query: 241 HDTQFALFGAGAEQDEPVLSSGTWEILMVRSAQVNTPLLSHYAGSTCELDSQPGRYNPGM 300
           HDTQFALFGAGAEQDEPVLSSGTWEILMVRSAQVNTPLLSHYAGSTCELDSQPGRYNPGM
Sbjct: 241 HDTQFALFGAGAEQDEPVLSSGTWEILMVRSAQVNTPLLSHYAGSTCELDSQPGRYNPGM 300

Query: 301 QWLASGVLEWVRQLLWTPETPWQTLIDEARALPDGAQKVKMQCDLLSSPNAGWQGITLNT 360
           QWLASGVLEWVRQLLWTPETPWQTLIDEARALPDGAQKVKMQCDLLSSPNAGWQGITLNT
Sbjct: 301 QWLASGVLEWVRQLLWTPETPWQTLIDEARALPDGAQKVKMQCDLLSSPNAGWQGITLNT 360

Query: 361 TRGHFYLAALEGLAEQLANNLQTLQKIGHFNASELLLVGGGSRNALWNQIKANRLDIPIK 420
           TRGHFYLAALEGLAEQLANNLQTLQKIGHFNASELLLVGGGSRNALWNQIKANRLDIPIK
Sbjct: 361 TRGHFYLAALEGLAEQLANNLQTLQKIGHFNASELLLVGGGSRNALWNQIKANRLDIPIK 420

Query: 421 VLDDAETTVAGAAMFGWYGVGEFSSPEQARAQVSYQYRYFYPQTEPELIEGV 472
           VLDDAETTVAGAAMFGWYGVGEFSSPEQARAQVSYQYRYFYPQTEPELIEGV
Sbjct: 421 VLDDAETTVAGAAMFGWYGVGEFSSPEQARAQVSYQYRYFYPQTEPELIEGV 472


Lambda     K      H
   0.319    0.133    0.406 

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: 913
Number of extensions: 29
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: 472
Length adjustment: 33
Effective length of query: 439
Effective length of database: 439
Effective search space:   192721
Effective search space used:   192721
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 BWI76_RS22930 BWI76_RS22930 (L-fuculokinase)
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.14904.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.9e-234  764.7   0.2   2.2e-234  764.5   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22930  BWI76_RS22930 L-fuculokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22930  BWI76_RS22930 L-fuculokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  764.5   0.2  2.2e-234  2.2e-234       2     465 .]       5     463 ..       4     463 .. 1.00

  Alignments for each domain:
  == domain 1  score: 764.5 bits;  conditional E-value: 2.2e-234
                               TIGR02628   2 vvlvldcGatnlraiainekGkivasasvknetkqaiensdyhiwdleeilqklvecaqkvqaevdekdil 72 
                                             v+lvldcGatn+raia++++G+i+a+a ++n++++a+ens +h+w+le+ilq+++ec++++ + ++ + ++
  lcl|FitnessBrowser__Koxy:BWI76_RS22930   5 VILVLDCGATNVRAIAVDRRGNIIARAATTNASDIAVENSAWHQWSLEAILQRFAECCRQISDPLSSCTVR 75 
                                             9********************************************************************** PP

                               TIGR02628  73 giavttfGvdGapfdeqgnqlypiiswkcprtvpvmenvereldakrlyrrnGiGdysfntlyklrwlkeh 143
                                             gi+vttfGvdGa++deqg++lyp+iswkcprt++vm+n++r + a++l++++G+G+++fntlykl wlke+
  lcl|FitnessBrowser__Koxy:BWI76_RS22930  76 GITVTTFGVDGALVDEQGKLLYPVISWKCPRTAAVMDNISRFMPAQQLQQISGVGAFAFNTLYKLIWLKEN 146
                                             *********************************************************************** PP

                               TIGR02628 144 kpqllekmdkfvfisslithrltGefttditmaGtsmmtdltsrnfdpailealGlseelfpplveaGeki 214
                                             +pqllek+ +++fissl+++rltGefttditmaGts+m+d+ +r+f+ +il+a+Gl+++lfp+lveaG++i
  lcl|FitnessBrowser__Koxy:BWI76_RS22930 147 HPQLLEKARAWLFISSLLNQRLTGEFTTDITMAGTSQMLDIHQRDFSTQILQATGLPRRLFPRLVEAGQQI 217
                                             *********************************************************************** PP

                               TIGR02628 215 GklrsdlakllGlnadvpvisaGhdtqfalfGsGaeenqpvlssGtweilmarsqraelslealsaGvtve 285
                                             G+l+sd+ak+lGl++++pvisaGhdtqfalfG+Gae+++pvlssGtweilm+rs+++++ l + +aG+t+e
  lcl|FitnessBrowser__Koxy:BWI76_RS22930 218 GTLQSDAAKMLGLAVGIPVISAGHDTQFALFGAGAEQDEPVLSSGTWEILMVRSAQVNTPLLSHYAGSTCE 288
                                             *********************************************************************** PP

                               TIGR02628 286 ldsqaglynpavqwlasgvvewvakllftaetasdelykvlieearkvangakgvvnletdlsslgqgaie 356
                                             ldsq g ynp++qwlasgv+ewv++ll+t et+    +++li+ear + +ga++v+ +++dl s  +++++
  lcl|FitnessBrowser__Koxy:BWI76_RS22930 289 LDSQPGRYNPGMQWLASGVLEWVRQLLWTPETP----WQTLIDEARALPDGAQKVK-MQCDLLSSPNAGWQ 354
                                             *********************************....******************9.************** PP

                               TIGR02628 357 GlslfttrGeiyraaleglakklkrrldvlekvsqlkakelvvvGGGsknvlwnqiranaldlpvkvvdda 427
                                             G++l+ttrG++y aalegla++l ++l+ l+k+++++a+el++vGGGs+n lwnqi+an ld+p+kv+dda
  lcl|FitnessBrowser__Koxy:BWI76_RS22930 355 GITLNTTRGHFYLAALEGLAEQLANNLQTLQKIGHFNASELLLVGGGSRNALWNQIKANRLDIPIKVLDDA 425
                                             *********************************************************************** PP

                               TIGR02628 428 eatvlGaalfafaGvGiyedveeaqaqlkpslrvvyps 465
                                             e+tv+Gaa+f+++GvG++ ++e+a+aq+ +++r++yp+
  lcl|FitnessBrowser__Koxy:BWI76_RS22930 426 ETTVAGAAMFGWYGVGEFSSPEQARAQVSYQYRYFYPQ 463
                                             *************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (465 nodes)
Target sequences:                          1  (472 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.61
//
[ok]

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
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