Alignments for a candidate for glpK in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Dyella japonica UNC79MFTsu3.2

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate N515DRAFT_3907 N515DRAFT_3907 glycerol kinase

Query= SwissProt::O66131
         (496 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3907
          Length = 499

 Score =  730 bits (1884), Expect = 0.0
 Identities = 350/492 (71%), Positives = 410/492 (83%)

Query: 4   YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63
           Y+LAIDQGTTSSRAILF+  G IV  AQ+EF Q FPQPGWVEHN  EI  SVL  +   +
Sbjct: 5   YILAIDQGTTSSRAILFDHDGHIVGTAQREFPQVFPQPGWVEHNPREIMTSVLVTMTEAI 64

Query: 64  SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123
           ++A V P ++AGIGITNQRET VVW+++TG PI+NAIVWQSRQT+ IC  L+ +GYD L 
Sbjct: 65  NQAGVDPARIAGIGITNQRETAVVWDRETGQPIHNAIVWQSRQTSEICTRLQQEGYDELV 124

Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183
           R KTGLLIDAYFSGTKV+WILDHVDGA+ RAERGELLFGTIDTWLIW L+GG+VHVTDY+
Sbjct: 125 RGKTGLLIDAYFSGTKVRWILDHVDGAQARAERGELLFGTIDTWLIWNLTGGKVHVTDYT 184

Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243
           NASRTL+++I+  +WDDELL +L +P+AMLPEV+ SSE+Y +T P HFFG EVPIAG AG
Sbjct: 185 NASRTLIYDIYKQQWDDELLKMLDIPRAMLPEVKSSSEIYGQTLPKHFFGREVPIAGIAG 244

Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALEG 303
           DQQAALFGQACF  G+AKNTYGTGCFMLMNTGEKAV SK+GLLTTIAWGIDGKVEYALEG
Sbjct: 245 DQQAALFGQACFEPGLAKNTYGTGCFMLMNTGEKAVPSKNGLLTTIAWGIDGKVEYALEG 304

Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363
           SIFVAGS IQWLRDGLRM+  A+DS+ YAE+   +DGVY VPAF+GLG PYW S+VRGAV
Sbjct: 305 SIFVAGSVIQWLRDGLRMLGKASDSQDYAERARDSDGVYFVPAFVGLGAPYWRSDVRGAV 364

Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQFQSD 423
           FGL+RGTTKE FIRA LES+AYQT+DVL  M+ D+GI L  LR DGGA+ N+F+ QFQ+D
Sbjct: 365 FGLSRGTTKEQFIRAALESMAYQTRDVLEAMQNDAGIELKELRADGGAIANDFMAQFQAD 424

Query: 424 LLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTMLYD 483
           +L V + RP V ETTA GAAYLAGLAVG+W SR++IA +W ++R F+P M  +KR  LY 
Sbjct: 425 ILDVTLLRPKVQETTAQGAAYLAGLAVGFWQSREEIARRWAVDREFKPSMAQEKREKLYG 484

Query: 484 GWKKAVRAAMAF 495
           GWKKAVRA M F
Sbjct: 485 GWKKAVRATMEF 496


Lambda     K      H
   0.319    0.134    0.406 

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: 874
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: 496
Length of database: 499
Length adjustment: 34
Effective length of query: 462
Effective length of database: 465
Effective search space:   214830
Effective search space used:   214830
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 N515DRAFT_3907 N515DRAFT_3907 (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.28595.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.3e-230  750.1   0.1   4.9e-230  749.9   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907  N515DRAFT_3907 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3907  N515DRAFT_3907 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.9   0.1  4.9e-230  4.9e-230       2     495 ..       5     495 ..       4     496 .. 0.99

  Alignments for each domain:
  == domain 1  score: 749.9 bits;  conditional E-value: 4.9e-230
                                    TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleik 67 
                                                  +i+aiDqGttssrai+fd++g++v++aq+e+ q+fp++gwvEh+p ei++sv+ +++ea+++++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907   5 YILAIDQGTTSSRAILFDHDGHIVGTAQREFPQVFPQPGWVEHNPREIMTSVLVTMTEAINQAGVD 70 
                                                  9***************************************************************** PP

                                    TIGR01311  68 aeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYf 133
                                                  ++ ia iGitnqREt+vvWd+etg+p++naivWq+++t++i+++l++e+++e +r ktGL++++Yf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907  71 PARIAGIGITNQRETAVVWDRETGQPIHNAIVWQSRQTSEICTRLQQEGYDELVRGKTGLLIDAYF 136
                                                  ****************************************************************** PP

                                    TIGR01311 134 satKlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdee 199
                                                  s+tK+rW+ld+v++++++ae+gellfGt+dtwli++Ltggkvhvtd+tNASRtl++++ +++wd+e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 137 SGTKVRWILDHVDGAQARAERGELLFGTIDTWLIWNLTGGKVHVTDYTNASRTLIYDIYKQQWDDE 202
                                                  ****************************************************************** PP

                                    TIGR01311 200 llelfkipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtG 265
                                                  ll++++ip+++lPe++ssse+yg++ +k+++++evpi+g++Gdqqaal+gq+c+++g aKntYgtG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 203 LLKMLDIPRAMLPEVKSSSEIYGQTLPKHFFGREVPIAGIAGDQQAALFGQACFEPGLAKNTYGTG 268
                                                  ****************************************************************** PP

                                    TIGR01311 266 cFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeevekl 331
                                                  cF+l+ntGek+v sk+glLtt+a+ ++gk    yalEGs++vaG+++qwlrd l+++ ka++++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 269 CFMLMNTGEKAVPSKNGLLTTIAWGIDGKVE--YALEGSIFVAGSVIQWLRDGLRMLGKASDSQDY 332
                                                  ***************************9985..********************************* PP

                                    TIGR01311 332 aksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekd 397
                                                  a+++ ds+gvyfVPaf GL+aPyW+sd rg+++Gl+r+ttke+++raale++a+q+rd+leam++d
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 333 AERARDSDGVYFVPAFVGLGAPYWRSDVRGAVFGLSRGTTKEQFIRAALESMAYQTRDVLEAMQND 398
                                                  ****************************************************************** PP

                                    TIGR01311 398 agvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksa 463
                                                  ag+e+k+L++DGg+++n+++ q+qadil+v++ rpkv+etta GaA++aglavg+w+s ee+++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 399 AGIELKELRADGGAIANDFMAQFQADILDVTLLRPKVQETTAQGAAYLAGLAVGFWQSREEIARRW 464
                                                  ****************************************************************** PP

                                    TIGR01311 464 eaeektfepemdeeerekkykkwkeaverslk 495
                                                  +++ ++f+p+m +e+rek y  wk+av+ +++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3907 465 AVD-REFKPSMAQEKREKLYGGWKKAVRATME 495
                                                  **8.***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (499 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.45
//
[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