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

GapMind for catabolism of small carbon sources

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

Align glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_007733474.1 C1M55_RS23175 glycerol kinase GlpK

Query= BRENDA::D0VZG4
         (505 letters)



>NCBI__GCF_002893965.1:WP_007733474.1
          Length = 502

 Score =  771 bits (1990), Expect = 0.0
 Identities = 368/502 (73%), Positives = 424/502 (84%)

Query: 1   MADYVLAIDQGTTSSRAIVFNHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVG 60
           MA +V AIDQGTTS+R ++F+HSG + +  Q EH QIFP+AGWVEH+P +IW+NVR V  
Sbjct: 1   MAQFVAAIDQGTTSTRCMIFDHSGHVVAVEQHEHTQIFPQAGWVEHDPIEIWDNVRNVTA 60

Query: 61  LALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGA 120
            AL   +LT  DIA+VGITNQRETAVVW++ TGKPVYNAIVWQDTRT +I   L G++G 
Sbjct: 61  GALANADLTAADIASVGITNQRETAVVWERATGKPVYNAIVWQDTRTDRICTALAGEDGP 120

Query: 121 EKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGV 180
            KY  + GLPLATYFSGPK+KWILDNVEG+REKAE G+L FG  DTWVLWNMTGG +GGV
Sbjct: 121 RKYTEVTGLPLATYFSGPKVKWILDNVEGSREKAEAGELCFGTMDTWVLWNMTGGVDGGV 180

Query: 181 HVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSEVYGHGRPRGLVPGVPI 240
           H TD TNASRT+LMDLDTL+W   I ADMGIP SMLP+IRSSSE +G  R RG + GVPI
Sbjct: 181 HATDPTNASRTLLMDLDTLAWDSAICADMGIPESMLPEIRSSSETFGFVRERGTLSGVPI 240

Query: 241 AGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIGDAPA 300
           AGILGDQQAATFGQAC   G+AKNTYGTGNF+LLNTGTEKVMSKNGLLTTVCYKIG+ P 
Sbjct: 241 AGILGDQQAATFGQACLSPGEAKNTYGTGNFVLLNTGTEKVMSKNGLLTTVCYKIGEQPT 300

Query: 301 VYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAPYWRP 360
           VYALEGSIAVTGSLVQWLRDNLGM ++A D+E  A  V DNGGAYFVPAFSGLFAP+WR 
Sbjct: 301 VYALEGSIAVTGSLVQWLRDNLGMIDNAADIEVNARSVDDNGGAYFVPAFSGLFAPHWRA 360

Query: 361 DARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVANELL 420
           DARGA+VGLTR+VN+ H+ARA LEATA+QSREV++AMN DSGVDL  L+VDGGMVANELL
Sbjct: 361 DARGAIVGLTRFVNKGHLARAVLEATAYQSREVIEAMNLDSGVDLKVLKVDGGMVANELL 420

Query: 421 MQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSMESGE 480
           MQFQAD L V+V+RP VAETTALGAAYAAG+AVG+W+ E D+  NWA+DK W+PSM+S E
Sbjct: 421 MQFQADLLDVEVIRPVVAETTALGAAYAAGLAVGYWESEDDIRSNWAKDKSWTPSMDSAE 480

Query: 481 RERLYRNWKKAVTKTMEWVDED 502
           RERLY  W+KAVT+T++WVD D
Sbjct: 481 RERLYAGWQKAVTRTLDWVDAD 502


Lambda     K      H
   0.316    0.134    0.408 

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: 937
Number of extensions: 28
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: 505
Length of database: 502
Length adjustment: 34
Effective length of query: 471
Effective length of database: 468
Effective search space:   220428
Effective search space used:   220428
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_007733474.1 C1M55_RS23175 (glycerol kinase GlpK)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

# 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/TIGR01311.hmm
# target sequence database:        /tmp/gapView.843940.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01311  [M=496]
Accession:   TIGR01311
Description: glycerol_kin: glycerol kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.1e-228  742.4   2.2     1e-227  742.2   2.2    1.0  1  NCBI__GCF_002893965.1:WP_007733474.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_007733474.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.2   2.2    1e-227    1e-227       1     496 []       3     498 ..       3     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 742.2 bits;  conditional E-value: 1e-227
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           +++aaiDqGtts+r+++fd++g++va +q+e++qifp++gwvEhdp ei+++v++v a al++++ +a++ia+
  NCBI__GCF_002893965.1:WP_007733474.1   3 QFVAAIDQGTTSTRCMIFDHSGHVVAVEQHEHTQIFPQAGWVEHDPIEIWDNVRNVTAGALANADLTAADIAS 75 
                                           69*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           +GitnqREt+vvW+++tgkp++naivWqdtrt +i+++l+ e   ++ +e tGLpl tYfs+ K++W+ldnve
  NCBI__GCF_002893965.1:WP_007733474.1  76 VGITNQRETAVVWERATGKPVYNAIVWQDTRTDRICTALAGEDGPRKYTEVTGLPLATYFSGPKVKWILDNVE 148
                                           *******************************************9***************************** PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtgg...kvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirs 216
                                           + r++ae+gel+fGt+dtw+++++tgg   +vh+td tNASRtll++l+tl+wd+ +++ ++ip+++lPeirs
  NCBI__GCF_002893965.1:WP_007733474.1 149 GSREKAEAGELCFGTMDTWVLWNMTGGvdgGVHATDPTNASRTLLMDLDTLAWDSAICADMGIPESMLPEIRS 221
                                           **************************99999****************************************** PP

                             TIGR01311 217 ssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvay 289
                                           sse++g ++e+  + ++vpi+g+lGdqqaa +gq+cl++geaKntYgtG+F+llntG++kv+sk+glLttv+y
  NCBI__GCF_002893965.1:WP_007733474.1 222 SSETFGFVRER-GTLSGVPIAGILGDQQAATFGQACLSPGEAKNTYGTGNFVLLNTGTEKVMSKNGLLTTVCY 293
                                           ********999.999********************************************************** PP

                             TIGR01311 290 klggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgt 362
                                           k+g++ + +yalEGs+av+G++vqwlrdnl++i++a+++e  a+sv+d++g yfVPafsGLfaP+W++dArg+
  NCBI__GCF_002893965.1:WP_007733474.1 294 KIGEQPT-VYALEGSIAVTGSLVQWLRDNLGMIDNAADIEVNARSVDDNGGAYFVPAFSGLFAPHWRADARGA 365
                                           ***8775.***************************************************************** PP

                             TIGR01311 363 ivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkva 435
                                           ivGltr+++k h+ara+lea a+q+r+++eam+ d+gv++kvLkvDGg+++n+llmq+qad+l+v+v rp va
  NCBI__GCF_002893965.1:WP_007733474.1 366 IVGLTRFVNKGHLARAVLEATAYQSREVIEAMNLDSGVDLKVLKVDGGMVANELLMQFQADLLDVEVIRPVVA 438
                                           ************************************************************************* PP

                             TIGR01311 436 ettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           ettalGaA+aaglavg+w+se++++++++++ k+++p+md++ere+ y+ w++av+r+l+w
  NCBI__GCF_002893965.1:WP_007733474.1 439 ETTALGAAYAAGLAVGYWESEDDIRSNWAKD-KSWTPSMDSAERERLYAGWQKAVTRTLDW 498
                                           *****************************98.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (502 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: 21.11
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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