GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galK in Pedobacter sp. GW460-11-11-14-LB5

Align Galactokinase (EC 2.7.1.6) (characterized)
to candidate CA265_RS06125 CA265_RS06125 galactokinase

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



>FitnessBrowser__Pedo557:CA265_RS06125
          Length = 383

 Score =  763 bits (1969), Expect = 0.0
 Identities = 383/383 (100%), Positives = 383/383 (100%)

Query: 1   MNAQHLKNTFKKLFNAEPILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDD 60
           MNAQHLKNTFKKLFNAEPILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDD
Sbjct: 1   MNAQHLKNTFKKLFNAEPILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDD 60

Query: 61  EIHLFSESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLGA 120
           EIHLFSESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLGA
Sbjct: 61  EIHLFSESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLGA 120

Query: 121 GLSSSAAVECATGFALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQ 180
           GLSSSAAVECATGFALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQ
Sbjct: 121 GLSSSAAVECATGFALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQ 180

Query: 181 AIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYPNV 240
           AIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYPNV
Sbjct: 181 AIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYPNV 240

Query: 241 STLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFETHE 300
           STLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFETHE
Sbjct: 241 STLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFETHE 300

Query: 301 GLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSSKY 360
           GLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSSKY
Sbjct: 301 GLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSSKY 360

Query: 361 LLQFGLKLDSYTVQTDNGTSLFN 383
           LLQFGLKLDSYTVQTDNGTSLFN
Sbjct: 361 LLQFGLKLDSYTVQTDNGTSLFN 383


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: 625
Number of extensions: 18
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 CA265_RS06125 CA265_RS06125 (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.575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.3e-106  341.9   0.0   2.8e-106  341.6   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS06125  CA265_RS06125 galactokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS06125  CA265_RS06125 galactokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.6   0.0  2.8e-106  2.8e-106       2     384 ..       4     378 ..       3     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 341.6 bits;  conditional E-value: 2.8e-106
                                  TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanad 69 
                                                +++k++F + ++++p + vr+PGR+n+iGeh+DYn+g+v+P aid  ++va+ +r d ++++ ++ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS06125   4 QHLKNTFKKLFNAEP-ILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGDDEIHLFSESYQ 70 
                                                567889999998876.789***********************************************99 PP

                                  TIGR00131  70 nklaerkldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaa 137
                                                 +++  +++  l+kse + WanY+ g   +l+eR ++ + G++ +i+gdvP gaGLsssaa+e+a + 
  lcl|FitnessBrowser__Pedo557:CA265_RS06125  71 -QFDISSINS-LKKSE-NSWANYILGIADQLKERGYQLG-GFNFYIDGDVPLGAGLSSSAAVECATGF 134
                                                .999999986.67778.89*******************9.**************************** PP

                                  TIGR00131 138 vlknlgkleldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleia 205
                                                 l +l++l ++  +i+l +qk+e+ f GvncG+mDq+asv+G++d a+++++r++k  +++l   +  
  lcl|FitnessBrowser__Pedo557:CA265_RS06125 135 ALDQLFSLSVSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKKDQAIMLDCRSMKHIYIPLKLDGYK 202
                                                ***************************************************************99*** PP

                                  TIGR00131 206 lviantnvksnlapseYnlRrqeveeaakvlakk.sekgaLrDvkeeefaryearltkllqlvekqRa 272
                                                l++ ntnvk+ la+s Yn Rr ++e+++  ++++  + ++LrDv  +  +     ++ ++ +v + + 
  lcl|FitnessBrowser__Pedo557:CA265_RS06125 203 LLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHyPNVSTLRDVDLTMLE---TYVKPMDLEVYN-KC 266
                                                ***************************99999884688999999988888...778899999998.9* PP

                                  TIGR00131 273 khvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGa 340
                                                + vv e  R l a++ l++++l+ lGkLm e ++ l +dye+++ e+d lve+++  + + G+R+ G+
  lcl|FitnessBrowser__Pedo557:CA265_RS06125 267 RFVVEEIGRLLTAAEQLENGNLQALGKLMFETHEGLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGG 334
                                                ******************************************************************** PP

                                  TIGR00131 341 GfGGCtvalvpnenvekvrkalaekYekktdlklefavivskea 384
                                                GfGGCt+++v++e++ ++ + l+ kY  + +lkl+ + ++++++
  lcl|FitnessBrowser__Pedo557:CA265_RS06125 335 GFGGCTINIVKEEKIADLVEELSSKYLLQFGLKLDSYTVQTDNG 378
                                                *************************************9998877 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.32
//
[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:

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:

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:

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:

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