Alignments for a candidate for galK in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Rhodococcus qingshengii djl-6-2

Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate WP_050656780.1 C1M55_RS27930 galactokinase

Query= curated2:Q7U1L7
         (363 letters)



>NCBI__GCF_002893965.1:WP_050656780.1
          Length = 376

 Score =  256 bits (654), Expect = 7e-73
 Identities = 149/357 (41%), Positives = 203/357 (56%), Gaps = 8/357 (2%)

Query: 5   YGAPGRVNLIGEHTDYNLGFALPIALPRRTVVTFTPEHTGAITARSDRADGSARIPLDTT 64
           + APGRVNLIGEHTDYN G  LP+AL +RT+V       G +   S ++  +   PL   
Sbjct: 25  WAAPGRVNLIGEHTDYNGGLCLPVALEQRTLVAVALRSDGVVRVHSRQSAETYTGPLGDI 84

Query: 65  PGQVTGWAAYAAGAIWALRGAGHPVPGGAMSITSDVEIGSGLSSSAALIGAVLGAVGAAT 124
                GWAAY    +W+L   G P+ G  +++ S V +G+GLSSSAAL  +V  AV    
Sbjct: 85  ---AAGWAAYPTAVLWSLARRGLPIEGIDLAVDSSVPVGAGLSSSAALTCSVALAVNELH 141

Query: 125 GTRIDRLERARLAQRAENDYVGAPTGLLDHLAALFGAPKTALLIDFRDITVRPVAFDPDA 184
            +   R E  ++  +AEND VGAPTG +D   ALF  P TALL+D +D +  P+ F+   
Sbjct: 142 DSPFARDELVQVCIQAENDGVGAPTGGMDQTIALFAQPSTALLLDCQDGSTEPIPFELHG 201

Query: 185 CDVVLLLMDSRARHRHAGGEYALRRASCERAAADLGVSSLR-AVQDRGLAALGAIADPID 243
               L+++D+R +H  A G+Y +RR+ C  AAA LGV SLR A  D+       + DPI 
Sbjct: 202 AGYELIVIDTRVKHSLADGQYGMRRSQCVAAAAALGVGSLREATADQA----ETVRDPIL 257

Query: 244 ARRARHVLTENQRVLDFAAALADSDFTAAGQLLTASHESMREDFAITTERIDLIAESAVR 303
             RARHV+TE +R    A  L  S F+  G+L   SH S+R+DF ++ + +D+   +A R
Sbjct: 258 RARARHVVTEIERTRKTAELLRSSRFSDVGELFDNSHASLRDDFEVSCDELDVAVAAARR 317

Query: 304 AGALGARMTGGGFGGAVIALVPADRARDVADTVRRAAVTAGYDEPAVSRTYAAPGAA 360
            GA+GARMTGGGFGG+ IALVP     +V  +V R     G+  P      A   AA
Sbjct: 318 GGAIGARMTGGGFGGSAIALVPEGSGAEVIASVSRDFAARGWRAPHFLGVVAGGSAA 374


Lambda     K      H
   0.320    0.134    0.390 

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: 252
Number of extensions: 8
Number of successful extensions: 3
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: 363
Length of database: 376
Length adjustment: 30
Effective length of query: 333
Effective length of database: 346
Effective search space:   115218
Effective search space used:   115218
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: 49 (23.5 bits)

Align candidate WP_050656780.1 C1M55_RS27930 (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.2358625.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.3e-84  268.0   0.0    8.1e-84  267.7   0.0    1.1  1  NCBI__GCF_002893965.1:WP_050656780.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050656780.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.7   0.0   8.1e-84   8.1e-84       3     364 ..       8     352 ..       6     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 8.1e-84
                             TIGR00131   3 evkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaer 75 
                                           +v + F  +y+++++ v  aPGRvnliGeh+DYn+g  lP+a++  tlvav+ r d  v++ + +        
  NCBI__GCF_002893965.1:WP_050656780.1   8 SVLQQFHATYGYPATGVWAAPGRVNLIGEHTDYNGGLCLPVALEQRTLVAVALRSDGVVRVHSRQSA-----E 75 
                                           78899********************************************************998876.....3 PP

                             TIGR00131  76 kldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlknlgkleld 148
                                            +  pl +     Wa Y+ +vl  l +R   ++ G+d+ +++ vP gaGLsssaal++ va  +++l++++  
  NCBI__GCF_002893965.1:WP_050656780.1  76 TYTGPLGDIA-AGWAAYPTAVLWSLARRGLPIE-GIDLAVDSSVPVGAGLSSSAALTCSVALAVNELHDSPFA 146
                                           4555665555.89****************9998.*************************************** PP

                             TIGR00131 149 skeillriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpql..eialviantnvksnlap 219
                                             e ++   ++e+  vG+ +GgmDq ++ + +   all++++   ++p++++    +  l++++t vk+ la+
  NCBI__GCF_002893965.1:WP_050656780.1 147 RDELVQVCIQAENDGVGAPTGGMDQTIALFAQPSTALLLDCQDGSTEPIPFELHgaGYELIVIDTRVKHSLAD 219
                                           ******************************************88888887776655999************** PP

                             TIGR00131 220 seYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkde 292
                                           ++Y +Rr ++  aa +l +     +Lr+ +  + +       ++   + + Ra+hvv+e +R+ k+++ll+  
  NCBI__GCF_002893965.1:WP_050656780.1 220 GQYGMRRSQCVAAAAALGVG----SLREATADQAE-------TVRDPILRARARHVVTEIERTRKTAELLRSS 281
                                           *****************998....99998876655.......444445556********************** PP

                             TIGR00131 293 dlkelGkLmnesqasldddyeitvpeidelvesialvnG.siGsRltGaGfGGCtvalvpnenvekvrkalae 364
                                            + ++G+L ++s+asl+dd+e+++ e+d  v ++a+  G  iG+R+tG+GfGG  +alvp++   +v+  ++ 
  NCBI__GCF_002893965.1:WP_050656780.1 282 RFSDVGELFDNSHASLRDDFEVSCDELD--VAVAAARRGgAIGARMTGGGFGGSAIALVPEGSGAEVIASVSR 352
                                           ****************************..5555555555********************8887777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (376 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: 00:00:00.00
# Mc/sec: 29.75
//
[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