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

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.4679.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: 7.25
//
[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