Alignments for a candidate for glpK in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Desulfacinum infernum DSM 9756

Align glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_073037044.1 BUB04_RS03660 glycerol kinase

Query= BRENDA::D0VZG4
         (505 letters)



>NCBI__GCF_900129305.1:WP_073037044.1
          Length = 503

 Score =  605 bits (1560), Expect = e-177
 Identities = 301/503 (59%), Positives = 370/503 (73%), Gaps = 3/503 (0%)

Query: 1   MADYVLAIDQGTTSSRAIVFNHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVG 60
           M  Y+ A+D GTTS+R I+F+  G I    Q EH QIFP  GWVEH+P +IW N + V+ 
Sbjct: 1   MGAYIGALDLGTTSNRFIIFDREGRIVGLDQKEHRQIFPNPGWVEHDPMEIWANTQAVIR 60

Query: 61  LALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGA 120
            AL++  L+  D+AA+GITNQRET VVWDKTTG+P YNAIVWQ TRT  I   L    G 
Sbjct: 61  GALSKTGLSGSDLAALGITNQRETTVVWDKTTGRPFYNAIVWQCTRTADICRGLEKTYGQ 120

Query: 121 EKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGV 180
           + ++   GLP+ATYFSGPKI+WIL+NV  A E A  G  LFG  ++W +W +TGG  GG 
Sbjct: 121 DGFRQKTGLPIATYFSGPKIRWILENVPEAAEAARNGTALFGTVESWAIWWLTGGPHGGA 180

Query: 181 HVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSE--VYGHGRPRGLVPG- 237
           HVTDVTNASRT+LM+L+TL W  +I   + IP+ MLP I  S +   +GH    G+    
Sbjct: 181 HVTDVTNASRTLLMNLETLDWDPEILDALEIPVQMLPRIVPSIDPNTWGHTVRTGVFQAT 240

Query: 238 VPIAGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIGD 297
           VP+ G LGDQQAA  GQ CF+ G+AKNTYGTG FLLLNTGT  V+S+ GLLTT+ Y++  
Sbjct: 241 VPVCGALGDQQAALVGQTCFQPGEAKNTYGTGCFLLLNTGTSPVVSQRGLLTTLGYQMRG 300

Query: 298 APAVYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAPY 357
              VY LEGSIA+ G+LVQWLRDNLG+ + A +VE LA  V+DNGGAY VPAFSGLFAPY
Sbjct: 301 HDPVYCLEGSIAIGGALVQWLRDNLGLIQTAAEVEDLARTVEDNGGAYLVPAFSGLFAPY 360

Query: 358 WRPDARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVAN 417
           WR DARG LVGLTR+VN+ H+ARA LEATA+Q+R++V+AM+ADSGV LT L+VDGGMVAN
Sbjct: 361 WRSDARGVLVGLTRFVNKGHLARAVLEATAYQTRDIVEAMDADSGVALTTLKVDGGMVAN 420

Query: 418 ELLMQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSME 477
           +LLMQ QAD L V VVRPKV ETTALGAAYAAG+AVG+W   Q++  NWA DK W+P+M+
Sbjct: 421 DLLMQIQADVLNVPVVRPKVTETTALGAAYAAGLAVGYWSDFQELSRNWAMDKTWTPAMD 480

Query: 478 SGERERLYRNWKKAVTKTMEWVD 500
              RE  YR WKKAV +T  W++
Sbjct: 481 EARREEGYRYWKKAVERTFGWLE 503


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: 854
Number of extensions: 28
Number of successful extensions: 2
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: 503
Length adjustment: 34
Effective length of query: 471
Effective length of database: 469
Effective search space:   220899
Effective search space used:   220899
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_073037044.1 BUB04_RS03660 (glycerol kinase)
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.940337.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-227  741.1   0.1   2.5e-227  741.0   0.1    1.0  1  NCBI__GCF_900129305.1:WP_073037044.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129305.1:WP_073037044.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  741.0   0.1  2.5e-227  2.5e-227       2     496 .]       4     501 ..       3     501 .. 0.99

  Alignments for each domain:
  == domain 1  score: 741.0 bits;  conditional E-value: 2.5e-227
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           +i+a+D Gtts+r+i+fd+eg++v+ +qke++qifp++gwvEhdp+ei++++++v++ al+k++ + +++aa+
  NCBI__GCF_900129305.1:WP_073037044.1   4 YIGALDLGTTSNRFIIFDREGRIVGLDQKEHRQIFPNPGWVEHDPMEIWANTQAVIRGALSKTGLSGSDLAAL 76 
                                           9************************************************************************ PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           GitnqREttvvWdk+tg+p +naivWq+trta+i++ l+++  ++ +r+ktGLp+ tYfs+ K+rW+l+nv+e
  NCBI__GCF_900129305.1:WP_073037044.1  77 GITNQRETTVVWDKTTGRPFYNAIVWQCTRTADICRGLEKTYGQDGFRQKTGLPIATYFSGPKIRWILENVPE 149
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtgg...kvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirss 217
                                           +++aa++g++lfGtv++w i+ Ltgg   ++hvtdvtNASRtll+nletl+wd e+l++++ip ++lP+i++s
  NCBI__GCF_900129305.1:WP_073037044.1 150 AAEAARNGTALFGTVESWAIWWLTGGphgGAHVTDVTNASRTLLMNLETLDWDPEILDALEIPVQMLPRIVPS 222
                                           *************************99999******************************************* PP

                             TIGR01311 218 se..vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttva 288
                                            +  ++g++ ++ +++++vp+ g+lGdqqaalvgq+c+++geaKntYgtGcFlllntG+++v+s+ glLtt++
  NCBI__GCF_900129305.1:WP_073037044.1 223 IDpnTWGHTVRTGVFQATVPVCGALGDQQAALVGQTCFQPGEAKNTYGTGCFLLLNTGTSPVVSQRGLLTTLG 295
                                           8755899999999************************************************************ PP

                             TIGR01311 289 yklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArg 361
                                           y++ g++p +y lEGs+a++Ga+vqwlrdnl+li++a+eve+la++ved++g y+VPafsGLfaPyW+sdArg
  NCBI__GCF_900129305.1:WP_073037044.1 296 YQMRGHDP-VYCLEGSIAIGGALVQWLRDNLGLIQTAAEVEDLARTVEDNGGAYLVPAFSGLFAPYWRSDARG 367
                                           *****998.**************************************************************** PP

                             TIGR01311 362 tivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkv 434
                                           ++vGltr+++k h+ara+lea a+q+rdi+eam++d+gv +++LkvDGg+++n+llmqiqad+l+v+v+rpkv
  NCBI__GCF_900129305.1:WP_073037044.1 368 VLVGLTRFVNKGHLARAVLEATAYQTRDIVEAMDADSGVALTTLKVDGGMVANDLLMQIQADVLNVPVVRPKV 440
                                           ************************************************************************* PP

                             TIGR01311 435 aettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           +ettalGaA+aaglavg+w++ +el+++++++ kt++p+mde++re+ y++wk+aver+ +w
  NCBI__GCF_900129305.1:WP_073037044.1 441 TETTALGAAYAAGLAVGYWSDFQELSRNWAMD-KTWTPAMDEARREEGYRYWKKAVERTFGW 501
                                           *******************************8.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (503 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.21
//
[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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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