Alignments for a candidate for glpK in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Derxia gummosa DSM 723

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_028311917.1 H566_RS0113945 glycerol kinase

Query= SwissProt::Q9WX53
         (496 letters)



>NCBI__GCF_000482785.1:WP_028311917.1
          Length = 498

 Score =  612 bits (1578), Expect = e-180
 Identities = 291/494 (58%), Positives = 370/494 (74%), Gaps = 1/494 (0%)

Query: 2   NQYILAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIAS 61
           +QYILA+DQGTTSSRA+LF++ G IV +AQKEF Q +PQPGWVEH+  +IW S     A 
Sbjct: 3   DQYILALDQGTTSSRAVLFDRAGRIVSVAQKEFPQIYPQPGWVEHDPADIWSSQAGTAAE 62

Query: 62  VLSEAQVKPEQVAGIGITNQRETTVVWVKDTGNPIYNAIVWQSRQTAGICDELKAKGYDP 121
            ++ A +    +A IGITNQRETT+VW ++TG P+YNAIVWQ R+TA  CD+LKA+G + 
Sbjct: 63  AVTHAGLNGAAIAAIGITNQRETTIVWDRETGKPVYNAIVWQDRRTADFCDQLKARGLEA 122

Query: 122 LFREKTGLLIDAYFSGTKVKWILDHVEGARERAERGELLFGTIDTWLIWKLSGGRAHVTD 181
             R +TGL ID+YFS TKV+WILD+V GARE AE G L FGT+D+WLIW  S G +HVTD
Sbjct: 123 AIRARTGLPIDSYFSATKVRWILDNVPGAREAAEAGRLAFGTVDSWLIWNFSRGGSHVTD 182

Query: 182 YSNASRTLMFNIHTLEWDDELLAILNVPKAMLPEVRPSSEVYAKTVPHHFFGVEVPIAGA 241
            +NA+RTL+FNIHTL+WD+ELLA+ ++P++MLP V  SSEV   T     F   +PIAG 
Sbjct: 183 VTNAARTLLFNIHTLQWDEELLALFDIPRSMLPRVTGSSEVIQPTETT-VFASRIPIAGI 241

Query: 242 AGDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVQSKHGLLTTIAWGIDGKVEYAL 301
           AGDQ AALFGQ C   GM KNTYGTGCF++MNTG + ++S++ L+TTIAW +  +V YAL
Sbjct: 242 AGDQHAALFGQMCLEPGMVKNTYGTGCFLMMNTGSQPIESRNNLVTTIAWKLGDEVTYAL 301

Query: 302 EGSIFVAGSAIQWLRDGLRMIKTAADSEAYAEKVESTDGVYVVPAFVGLGTPYWDSEVRG 361
           EGSIF+ G+ +QWLRDGL +I++A ++EA A  VESTDGVY+VPAF GLG P+W+   RG
Sbjct: 302 EGSIFIGGAVVQWLRDGLGLIRSAGETEALAASVESTDGVYLVPAFAGLGAPHWNPRARG 361

Query: 362 AVFGLTRGTTKEHFIRATLESLAYQTKDVLAAMEADSGISLTTLRVDGGAVKNNFLMQFQ 421
           +VFG+TRGTT  H +RA LE++AYQ+ DVL AMEAD+G  +  LRVDGGAV NN L++FQ
Sbjct: 362 SVFGITRGTTTAHLVRAALEAIAYQSVDVLKAMEADAGTPIRELRVDGGAVANNLLLRFQ 421

Query: 422 SDLLAVPVERPVINETTALGAPYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTML 481
           +D+L V V RP + ETTALGA YLAGLAVGYW    +I AQW  +RRF P +   +    
Sbjct: 422 ADMLGVDVVRPTVTETTALGAAYLAGLAVGYWKDVGEIRAQWAQDRRFAPDLPAAEVERR 481

Query: 482 YDGWKKAVRAAMAF 495
             GW +AV AA A+
Sbjct: 482 LAGWHRAVTAAKAW 495


Lambda     K      H
   0.319    0.134    0.405 

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: 806
Number of extensions: 32
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: 496
Length of database: 498
Length adjustment: 34
Effective length of query: 462
Effective length of database: 464
Effective search space:   214368
Effective search space used:   214368
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_028311917.1 H566_RS0113945 (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.25202.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-224  729.5   0.3   8.2e-224  729.4   0.3    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028311917.1  H566_RS0113945 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028311917.1  H566_RS0113945 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.4   0.3  8.2e-224  8.2e-224       1     496 []       4     495 ..       4     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 729.4 bits;  conditional E-value: 8.2e-224
                                 TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikae 69 
                                               ++i+a+DqGttssra++fd+ g++v+ aqke+ qi+p++gwvEhdp +i++s+  ++aea+++++ + +
  lcl|NCBI__GCF_000482785.1:WP_028311917.1   4 QYILALDQGTTSSRAVLFDRAGRIVSVAQKEFPQIYPQPGWVEHDPADIWSSQAGTAAEAVTHAGLNGA 72 
                                               69******************************************************************* PP

                                 TIGR01311  70 eiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKl 138
                                                iaaiGitnqREtt+vWd+etgkp++naivWqd+rta+++++lk+++ e  +r++tGLp+++YfsatK+
  lcl|NCBI__GCF_000482785.1:WP_028311917.1  73 AIAAIGITNQRETTIVWDRETGKPVYNAIVWQDRRTADFCDQLKARGLEAAIRARTGLPIDSYFSATKV 141
                                               ********************************************************************* PP

                                 TIGR01311 139 rWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkip 207
                                               rW+ldnv+++r+aae+g+l fGtvd+wli+++++g+ hvtdvtNA+Rtll+n++tl+wdeell+lf+ip
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 142 RWILDNVPGAREAAEAGRLAFGTVDSWLIWNFSRGGSHVTDVTNAARTLLFNIHTLQWDEELLALFDIP 210
                                               ********************************************************************* PP

                                 TIGR01311 208 kellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekk 276
                                               +++lP+++ ssev+  +e++ ++ +++pi+g++Gdq+aal+gq+cl++g++KntYgtGcFl++ntG+++
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 211 RSMLPRVTGSSEVIQPTETT-VFASRIPIAGIAGDQHAALFGQMCLEPGMVKNTYGTGCFLMMNTGSQP 278
                                               **************999999.99********************************************** PP

                                 TIGR01311 277 viskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVP 345
                                               + s+++l+tt+a+klg++ +  yalEGs++++Ga+vqwlrd l+li++a e+e+la sve+++gvy+VP
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 279 IESRNNLVTTIAWKLGDEVT--YALEGSIFIGGAVVQWLRDGLGLIRSAGETEALAASVESTDGVYLVP 345
                                               ****************9886..*********************************************** PP

                                 TIGR01311 346 afsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglskn 414
                                               af+GL+aP+W+++Arg ++G+tr+tt++h++raalea+a+q+ d+l+ame+dag+ +++L+vDGg+++n
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 346 AFAGLGAPHWNPRARGSVFGITRGTTTAHLVRAALEAIAYQSVDVLKAMEADAGTPIRELRVDGGAVAN 414
                                               ********************************************************************* PP

                                 TIGR01311 415 nllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekky 483
                                               nll+++qad+lgv+v+rp+v+ettalGaA++aglavg+wk+  e++++++++ ++f+p+  ++e e+++
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 415 NLLLRFQADMLGVDVVRPTVTETTALGAAYLAGLAVGYWKDVGEIRAQWAQD-RRFAPDLPAAEVERRL 482
                                               **************************************************98.**************** PP

                                 TIGR01311 484 kkwkeaverslkw 496
                                               + w++av+ ++ w
  lcl|NCBI__GCF_000482785.1:WP_028311917.1 483 AGWHRAVTAAKAW 495
                                               ********99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (498 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: 8.77
//
[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 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