Alignments for a candidate for galK in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Echinicola vietnamensis KMM 6221, DSM 17526

Align Galactokinase (EC 2.7.1.6) (characterized)
to candidate Echvi_0696 Echvi_0696 galactokinase

Query= reanno::Pedo557:CA265_RS06125
         (383 letters)



>FitnessBrowser__Cola:Echvi_0696
          Length = 383

 Score =  381 bits (979), Expect = e-110
 Identities = 187/379 (49%), Positives = 259/379 (68%)

Query: 1   MNAQHLKNTFKKLFNAEPILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDD 60
           MN   +++ F++LF+ +PI+V+SPGRIN+IGEHTDYN GFV+PAAI+K I +A+ K   D
Sbjct: 1   MNPGIIRSAFEELFDKKPIVVKSPGRINLIGEHTDYNEGFVLPAAINKEIVIAVQKNDSD 60

Query: 61  EIHLFSESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLGA 120
           E  LFS+ +Q+     ++  ++ E  W NY++G+  QL++ GY + GF+    GDVP+GA
Sbjct: 61  ECRLFSQDFQESLTFDLHDFERMEGGWGNYVMGVVAQLQQAGYPIEGFDLVFGGDVPVGA 120

Query: 121 GLSSSAAVECATGFALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQ 180
           GLSSSAAVE     AL +LF L + R+D+   AQKAE  FAGV CGIMDQFAS+ GK + 
Sbjct: 121 GLSSSAAVENGVCLALSELFGLGLERLDMLKFAQKAEHEFAGVQCGIMDQFASMMGKDNH 180

Query: 181 AIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYPNV 240
           AI LDCRS+++ Y P+ L  Y+++L +T VKH+LADSAYN RR +C+ GVA V+     V
Sbjct: 181 AIRLDCRSLEYSYFPIDLGDYQIILCDTQVKHSLADSAYNDRRRECQAGVAAVQQTNQTV 240

Query: 241 STLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFETHE 300
            +LRDV L +LE     +   V+ +C+FV+EE  RLL   E LE G+++  G+ M+ +H+
Sbjct: 241 KSLRDVTLELLEETKSKISEVVFRRCKFVIEENARLLKGCELLEKGDIKGFGQQMYGSHD 300

Query: 301 GLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSSKY 360
           GLS  YEVSCKELDFL +  K  + V GARMMGGGFGGCTIN+V++       +E+++ Y
Sbjct: 301 GLSGLYEVSCKELDFLADFAKSRETVAGARMMGGGFGGCTINLVEKGAKETFEKEVAAAY 360

Query: 361 LLQFGLKLDSYTVQTDNGT 379
              FG  L  Y V+  +GT
Sbjct: 361 EKAFGKSLQIYEVEVTDGT 379


Lambda     K      H
   0.319    0.136    0.393 

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: 392
Number of extensions: 14
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: 383
Length of database: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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: 50 (23.9 bits)

Align candidate Echvi_0696 Echvi_0696 (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.2118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   6.2e-103  330.6   0.0   7.3e-103  330.4   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0696  Echvi_0696 galactokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0696  Echvi_0696 galactokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.4   0.0  7.3e-103  7.3e-103       4     386 ..       6     380 ..       4     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 330.4 bits;  conditional E-value: 7.3e-103
                            TIGR00131   4 vkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkl 77 
                                          ++++F + +++kp +vv++PGR+nliGeh+DYn+g+vlP ai+ ++++av++ d  + ++ +++++   +   +
  lcl|FitnessBrowser__Cola:Echvi_0696   6 IRSAFEELFDKKP-IVVKSPGRINLIGEHTDYNEGFVLPAAINKEIVIAVQKNDSDECRLFSQDFQ---ESLTF 75 
                                          5678999999887.899*************************************************...56678 PP

                            TIGR00131  78 dlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleldske 151
                                          dl   ++    W nYv gv+ +lq+  + ++ G+d+v+ gdvP gaGLsssaa+e  v   l +l+ l l+  +
  lcl|FitnessBrowser__Cola:Echvi_0696  76 DLHDFERMEGGWGNYVMGVVAQLQQAGYPIE-GFDLVFGGDVPVGAGLSSSAAVENGVCLALSELFGLGLERLD 148
                                          88777777789***************99999.****************************************** PP

                            TIGR00131 152 illriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlR 225
                                          +l+ +qk+e +f Gv cG+mDq+as +G+++ha+ +++r+L++ +++++  +  +++ +t+vk+ la+s Yn R
  lcl|FitnessBrowser__Cola:Echvi_0696 149 MLKFAQKAEHEFAGVQCGIMDQFASMMGKDNHAIRLDCRSLEYSYFPIDLGDYQIILCDTQVKHSLADSAYNDR 222
                                          ************************************************************************** PP

                            TIGR00131 226 rqeveeaakvlakk.sekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelG 298
                                          r e++ ++ +++++ +   +LrDv+ e  +   +  +k++++v + R k v+ en+R lk  +ll+++d+k +G
  lcl|FitnessBrowser__Cola:Echvi_0696 223 RRECQAGVAAVQQTnQTVKSLRDVTLELLE---ETKSKISEVVFR-RCKFVIEENARLLKGCELLEKGDIKGFG 292
                                          *******99999882345689**9999888...999*******99.**************************** PP

                            TIGR00131 299 kLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdl 372
                                          + m  s++ l  +ye+++ e+d l   ++  + + G+R+ G+GfGGCt++lv+++  e+++k +a  Yek  + 
  lcl|FitnessBrowser__Cola:Echvi_0696 293 QQMYGSHDGLSGLYEVSCKELDFLADFAKSRETVAGARMMGGGFGGCTINLVEKGAKETFEKEVAAAYEKAFGK 366
                                          ************************************************************************** PP

                            TIGR00131 373 klefavivskealg 386
                                           l+ + ++  ++ +
  lcl|FitnessBrowser__Cola:Echvi_0696 367 SLQIYEVEVTDGTR 380
                                          *9999998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (383 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.88
//
[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