Alignments for a candidate for glpK in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Acidovorax sp. GW101-3H11

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate Ac3H11_789 Glycerol kinase (EC 2.7.1.30)

Query= SwissProt::O66131
         (496 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_789
          Length = 497

 Score =  558 bits (1439), Expect = e-163
 Identities = 271/495 (54%), Positives = 356/495 (71%), Gaps = 5/495 (1%)

Query: 4   YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63
           Y+LA+DQGT+SSR+I+F+++G IV  AQ E  Q +PQPGWVEH+  EIW + LA     L
Sbjct: 3   YLLALDQGTSSSRSIVFDERGHIVAQAQLELPQIYPQPGWVEHDPLEIWRTQLATARDAL 62

Query: 64  SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123
           ++A +    V  +GITNQRETTV+W + TG P+++AIVWQ R+    C +L+ +G+    
Sbjct: 63  AKAGLAASAVRAVGITNQRETTVLWNRQTGQPVHHAIVWQDRRAEPACAQLREQGHAATI 122

Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183
           + KTGLL+DAYFSGTK++W+LDHV GAR+ AERGEL FGT+D+WL+WKL+ G+VHVTD S
Sbjct: 123 QAKTGLLVDAYFSGTKLQWLLDHVPGARDAAERGELAFGTVDSWLMWKLTHGKVHVTDVS 182

Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243
           NASRT++FN+HT +WDDELL +L +PKA++PEV PS+  +  TA     G  + I G AG
Sbjct: 183 NASRTMLFNVHTNQWDDELLALLRIPKALMPEVLPSAAHFGDTAA-DLLGHAIRIGGVAG 241

Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALEG 303
           DQQ+ALFGQACFT GMAKNTYGTGCFMLM+TG     S++GLLTT A     + E+A+EG
Sbjct: 242 DQQSALFGQACFTAGMAKNTYGTGCFMLMHTGGSFQTSQNGLLTTSAAQATAQPEFAMEG 301

Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363
           S+FV G+ +QWLRDGLR I T+ + E+ A+ V  + GV +VPAF GLG PYW  + RG +
Sbjct: 302 SVFVGGAVVQWLRDGLRAISTSGEVESLAQSVPDSGGVMMVPAFTGLGAPYWKPDARGTI 361

Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADS----GISLTTLRVDGGAVKNNFLMQ 419
            GLTRGTT  H  RA LES+AYQ+  +L  M  D+    G  ++ LRVDGGA  N+ LMQ
Sbjct: 362 TGLTRGTTLGHIARAALESIAYQSAALLLAMSRDAVAAGGAPVSELRVDGGACINDLLMQ 421

Query: 420 FQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRT 479
           FQ+DLL +PV RP V ETTALGAAYLAGL+ G + S D+++  W+ +RRF P +   +  
Sbjct: 422 FQADLLGIPVVRPAVIETTALGAAYLAGLSSGVYRSTDELSQLWRADRRFVPTLSSARAQ 481

Query: 480 MLYDGWKKAVRAAMA 494
            L   W+ AVR  +A
Sbjct: 482 ELMANWEHAVRQTVA 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: 720
Number of extensions: 33
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: 496
Length of database: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
Effective search space:   213906
Effective search space used:   213906
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 Ac3H11_789 (Glycerol kinase (EC 2.7.1.30))
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.23283.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   4.2e-214  697.3   0.5   4.7e-214  697.2   0.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789  Glycerol kinase (EC 2.7.1.30)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789  Glycerol kinase (EC 2.7.1.30)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.2   0.5  4.7e-214  4.7e-214       2     494 ..       3     495 ..       2     497 .] 0.99

  Alignments for each domain:
  == domain 1  score: 697.2 bits;  conditional E-value: 4.7e-214
                                       TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekl 64 
                                                     +++a+DqGt+ssr ivfd++g++va+aq el qi+p++gwvEhdplei++++++++++al+k+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789   3 YLLALDQGTSSSRSIVFDERGHIVAQAQLELPQIYPQPGWVEHDPLEIWRTQLATARDALAKA 65 
                                                     89************************************************************* PP

                                       TIGR01311  65 eikaeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGL 127
                                                     +  a+ + a+GitnqREttv+W+++tg+p+++aivWqd+r +  +++l+e+++  ++++ktGL
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789  66 GLAASAVRAVGITNQRETTVLWNRQTGQPVHHAIVWQDRRAEPACAQLREQGHAATIQAKTGL 128
                                                     *************************************************************** PP

                                       TIGR01311 128 plstYfsatKlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtllln 190
                                                     ++++Yfs+tKl+Wlld+v+++r+aae+gel fGtvd+wl++kLt+gkvhvtdv+NASRt+l+n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 129 LVDAYFSGTKLQWLLDHVPGARDAAERGELAFGTVDSWLMWKLTHGKVHVTDVSNASRTMLFN 191
                                                     *************************************************************** PP

                                       TIGR01311 191 letlkwdeellelfkipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlcl 253
                                                     ++t++wd+ell+l++ipk+l+Pe+ +s++++g+++++ ll++++ i gv+Gdqq+al+gq+c+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 192 VHTNQWDDELLALLRIPKALMPEVLPSAAHFGDTAAD-LLGHAIRIGGVAGDQQSALFGQACF 253
                                                     ***********************************99.************************* PP

                                       TIGR01311 254 kkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlr 316
                                                     ++g+aKntYgtGcF+l++tG + ++s++glLtt a +   +   ++a+EGsv+v+Ga+vqwlr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 254 TAGMAKNTYGTGCFMLMHTGGSFQTSQNGLLTTSAAQATAQP--EFAMEGSVFVGGAVVQWLR 314
                                                     ************************************998766..6****************** PP

                                       TIGR01311 317 dnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraa 379
                                                     d l+ i+++ eve+la+sv+ds+gv++VPaf+GL+aPyW++dArgti+Gltr+tt  hiaraa
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 315 DGLRAISTSGEVESLAQSVPDSGGVMMVPAFTGLGAPYWKPDARGTITGLTRGTTLGHIARAA 377
                                                     *************************************************************** PP

                                       TIGR01311 380 leavafqardileamekdag....vevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                                     le++a+q+ ++l am++da     + v++L+vDGg++ n+llmq+qad+lg++v+rp v ett
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 378 LESIAYQSAALLLAMSRDAVaaggAPVSELRVDGGACINDLLMQFQADLLGIPVVRPAVIETT 440
                                                     *******************988888999*********************************** PP

                                       TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                                     alGaA++agl +gv++s++el++ ++a+ ++f p+ ++++ ++ +++w++av++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_789 441 ALGAAYLAGLSSGVYRSTDELSQLWRAD-RRFVPTLSSARAQELMANWEHAVRQTV 495
                                                     ***************************8.***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (497 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: 9.97
//
[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