Alignments for a candidate for galK in Vagococcus penaei CD276

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Vagococcus penaei CD276

Align galactose kinase (characterized)
to candidate WP_126844466.1 BW732_RS08170 galactokinase

Query= CharProtDB::CH_024146
         (382 letters)



>NCBI__GCF_001998885.1:WP_126844466.1
          Length = 389

 Score =  283 bits (723), Expect = 8e-81
 Identities = 159/385 (41%), Positives = 233/385 (60%), Gaps = 12/385 (3%)

Query: 5   EKTQSLFANAFGYPATHTIQAPGRVNLIGEHTDYNDGFVLPCAIDYQTVISCAPRDDRKV 64
           E     F   F         APGR+NLIGEHTDYN G V PCAI Y T      R+DR V
Sbjct: 3   ETLNETFIKIFNEKPESAYFAPGRINLIGEHTDYNGGNVFPCAISYGTYGVVKAREDRLV 62

Query: 65  RVMAADYENQ-LDEFSLDAPIVAHENYQWANYVRGVVKHL-QLRNN--SFGGVDMVISGN 120
           R+ + ++ +  + EFSLD  +   E   WANY +G++ +L  L +N  +  G D+VI G+
Sbjct: 63  RLYSMNFPDLGIKEFSLD-DLTYKEADNWANYPKGMIGYLYDLVDNKEAVTGFDVVIFGD 121

Query: 121 VPQGAGLSSSASLEVAVGTVLQQLYHLPLDGAQIALNGQEAENQFVGCNCGIMDQLISAL 180
           +P GAGLSSSAS+E+  G +++ L+ L LD  ++   GQ+ EN F+G N GIMDQ    +
Sbjct: 122 IPNGAGLSSSASIELLTGVIVEDLWQLTLDRVELVKLGQKVENHFIGVNSGIMDQFAIGM 181

Query: 181 GKKDHALLIDCRSLGTKAVSMP-KGVAVVIINSNFKRTLVGSEYNTRREQCETGARFFQQ 239
           G+KD A+L+DC +L  + V +  +   ++I+N+N +R L  S+YN RR +C+   R  Q 
Sbjct: 182 GQKDQAILLDCHTLNYEMVPVHLENEKILIMNTNKRRELADSKYNERRAECDEALRRLQT 241

Query: 240 ----PALRDVTIEEFNAVAHEL-DPIVAKRVRHILTENARTVEAASALEQGDLKRMGELM 294
                AL ++++ +F+ +   + D  + KR RH + EN RT+EA  ALE  DL+  GEL+
Sbjct: 242 VTDIQALGELSLAQFDELKAVIKDDTLEKRARHAVAENQRTLEAKQALEANDLQTFGELL 301

Query: 295 AESHASMRDDFEITVPQIDTLVEIVKAVIGDKGGVRMTGGGFGGCIVALIPEELVPAVQQ 354
             SH S+RDD+E+T  ++DT+V + +A  G   G RMTG GFGGC +AL+ E+ +P + Q
Sbjct: 302 NASHQSLRDDYEVTGQELDTIVALTQAQNG-VIGARMTGAGFGGCAIALVKEDKLPEIIQ 360

Query: 355 AVAEQYEAKTGIKETFYVCKPSQGA 379
           AV + Y+ K G +  FYV   + GA
Sbjct: 361 AVGKAYQEKIGYEADFYVASIADGA 385


Lambda     K      H
   0.318    0.134    0.389 

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: 356
Number of extensions: 14
Number of successful extensions: 6
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: 382
Length of database: 389
Length adjustment: 30
Effective length of query: 352
Effective length of database: 359
Effective search space:   126368
Effective search space used:   126368
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_126844466.1 BW732_RS08170 (galactokinase)
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

# 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/TIGR00131.hmm
# target sequence database:        /tmp/gapView.3482968.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00131  [M=388]
Accession:   TIGR00131
Description: gal_kin: galactokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-132  426.8   0.1   4.3e-132  426.6   0.1    1.0  1  NCBI__GCF_001998885.1:WP_126844466.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001998885.1:WP_126844466.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.6   0.1  4.3e-132  4.3e-132       2     387 ..       3     387 ..       2     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 426.6 bits;  conditional E-value: 4.3e-132
                             TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadn.kla 73 
                                           e+++++F++ ++ekp+   +aPGR+nliGeh+DYn+g v+P+ai ++t+  vk r+d+ v+++++n+ +  ++
  NCBI__GCF_001998885.1:WP_126844466.1   3 ETLNETFIKIFNEKPESAYFAPGRINLIGEHTDYNGGNVFPCAISYGTYGVVKAREDRLVRLYSMNFPDlGIK 75 
                                           567899*************************************************************888*** PP

                             TIGR00131  74 erkldlpldksevsdWanYvkgvlkvlqeRfnsvpl..GldivisgdvPtgaGLsssaalevavaavlknlgk 144
                                           e++ld+  +k+  ++WanY+kg +  l +   + +   G+d+vi gd+P+gaGLsssa++e++ ++++++l++
  NCBI__GCF_001998885.1:WP_126844466.1  76 EFSLDDLTYKEA-DNWANYPKGMIGYLYDLVDNKEAvtGFDVVIFGDIPNGAGLSSSASIELLTGVIVEDLWQ 147
                                           *****9988877.***********99995544433334*********************************** PP

                             TIGR00131 145 leldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnl 217
                                           l+ld  e ++ +qkve+hf+Gvn+G+mDq+a+++G++d a+l+++++L+++ v++   +  ++i+ntn++++l
  NCBI__GCF_001998885.1:WP_126844466.1 148 LTLDRVELVKLGQKVENHFIGVNSGIMDQFAIGMGQKDQAILLDCHTLNYEMVPVHLENEKILIMNTNKRREL 220
                                           *******************************************************999999************ PP

                             TIGR00131 218 apseYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllk 290
                                           a+s+Yn Rr e++ea++ l++ +++ aL++++ ++f+   +    ++  + ++Ra+h+v+en+R+l+a ++l+
  NCBI__GCF_001998885.1:WP_126844466.1 221 ADSKYNERRAECDEALRRLQTVTDIQALGELSLAQFD---ELKAVIKDDTLEKRARHAVAENQRTLEAKQALE 290
                                           *************************************...6666677777778******************** PP

                             TIGR00131 291 dedlkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCtvalvpnenvekvrkala 363
                                            +dl+++G+L+n+s++sl+ddye+t  e+d+ v + +++nG+iG+R+tGaGfGGC +alv++++++++++a++
  NCBI__GCF_001998885.1:WP_126844466.1 291 ANDLQTFGELLNASHQSLRDDYEVTGQELDTIVALTQAQNGVIGARMTGAGFGGCAIALVKEDKLPEIIQAVG 363
                                           ************************************************************************* PP

                             TIGR00131 364 ekYekktdlklefavivskealge 387
                                           + Y++k + +++f+v+ + +++++
  NCBI__GCF_001998885.1:WP_126844466.1 364 KAYQEKIGYEADFYVASIADGAKK 387
                                           *******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (389 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 13.78
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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