Alignments for a candidate for glpK in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Herbaspirillum seropedicae SmR1

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate HSERO_RS04875 HSERO_RS04875 glycerol kinase

Query= SwissProt::O66131
         (496 letters)



>FitnessBrowser__HerbieS:HSERO_RS04875
          Length = 495

 Score =  575 bits (1482), Expect = e-168
 Identities = 269/491 (54%), Positives = 359/491 (73%), Gaps = 1/491 (0%)

Query: 4   YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63
           Y+LA+DQGT+SSR+I+F+Q G IV  AQ+EF Q FPQPGWVEH+  ++W S L     VL
Sbjct: 3   YLLALDQGTSSSRSIIFDQSGAIVATAQQEFPQIFPQPGWVEHDPMDLWHSQLQTAQKVL 62

Query: 64  SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123
           +++ +K  ++  +GITNQRETTVVWE+ TG P+YNA+VWQ R+   +C  L+ +G     
Sbjct: 63  AQSGIKASELTALGITNQRETTVVWERATGKPVYNAVVWQDRRAEVVCAALRERGLGEAI 122

Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183
           +KKTGL++D YFSGTK++WILDHVDG R RAERGELLFGT+D+WL+W L+GGR+HV+D S
Sbjct: 123 QKKTGLVLDPYFSGTKLRWILDHVDGLRARAERGELLFGTVDSWLVWNLTGGRLHVSDVS 182

Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243
           NASRT+++NIHT  WD+ELL  LG+P AMLP+V+PS+ +Y +    H  G  V I G AG
Sbjct: 183 NASRTMLWNIHTGAWDEELLQWLGIPAAMLPQVQPSAHLYGEIDAQH-LGAAVKIGGIAG 241

Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALEG 303
           DQQ+ALFGQAC   GMAKNTYGTGCFML++TG++   S +GL++T A  +D + +YALEG
Sbjct: 242 DQQSALFGQACVRPGMAKNTYGTGCFMLLHTGDQCATSHNGLISTAACQVDEQKQYALEG 301

Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363
           S+F+ G+ +QWLRDGL+ IKT+ D E  A  VE + GV  VP+F GLG PYW+   +GA+
Sbjct: 302 SVFIGGAVVQWLRDGLKAIKTSTDVEGLACSVEDSGGVVFVPSFTGLGAPYWNPSAKGAI 361

Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQFQSD 423
            GL+RG+T  H  RA LES+A+Q+  +L  M  D+   +T LRVDGGA  NN L+QFQ+D
Sbjct: 362 VGLSRGSTVAHIARAALESIAFQSTALLNAMVRDAVSPITELRVDGGAAANNLLLQFQAD 421

Query: 424 LLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTMLYD 483
           LL +PV RP V ETTALGAAYLAG+A G +    ++++QW++E  FEP +  D+      
Sbjct: 422 LLGIPVIRPQVTETTALGAAYLAGIATGVYRDLSELSSQWRMEHTFEPSIGRDQAQARIH 481

Query: 484 GWKKAVRAAMA 494
            W+ A+R   A
Sbjct: 482 AWEAAIRQVSA 492


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: 744
Number of extensions: 23
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: 495
Length adjustment: 34
Effective length of query: 462
Effective length of database: 461
Effective search space:   212982
Effective search space used:   212982
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 HSERO_RS04875 HSERO_RS04875 (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.26833.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-216  705.7   0.6   1.5e-216  705.4   0.6    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS04875  HSERO_RS04875 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS04875  HSERO_RS04875 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.4   0.6  1.5e-216  1.5e-216       2     492 ..       3     489 ..       2     492 .. 0.99

  Alignments for each domain:
  == domain 1  score: 705.4 bits;  conditional E-value: 1.5e-216
                                  TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikae 69 
                                                +++a+DqGt+ssr i+fd++g +va+aq+e+ qifp++gwvEhdp+++++s++++++++l++++ika+
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875   3 YLLALDQGTSSSRSIIFDQSGAIVATAQQEFPQIFPQPGWVEHDPMDLWHSQLQTAQKVLAQSGIKAS 70 
                                                89****************************************************************** PP

                                  TIGR01311  70 eiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatK 137
                                                e++a+GitnqREttvvW+++tgkp++na+vWqd+r + ++++l+e++  e +++ktGL+l++Yfs+tK
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875  71 ELTALGITNQRETTVVWERATGKPVYNAVVWQDRRAEVVCAALRERGLGEAIQKKTGLVLDPYFSGTK 138
                                                ******************************************************************** PP

                                  TIGR01311 138 lrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfk 205
                                                lrW+ld+v+++r++ae+gellfGtvd+wl+++Ltgg+ hv+dv+NASRt+l n++t +wdeell+ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 139 LRWILDHVDGLRARAERGELLFGTVDSWLVWNLTGGRLHVSDVSNASRTMLWNIHTGAWDEELLQWLG 206
                                                ******************************************************************** PP

                                  TIGR01311 206 ipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntG 273
                                                ip+++lP++++s++ ygei+++ +l+++v+i g++Gdqq+al+gq+c+++g+aKntYgtGcF+ll+tG
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 207 IPAAMLPQVQPSAHLYGEIDAQ-HLGAAVKIGGIAGDQQSALFGQACVRPGMAKNTYGTGCFMLLHTG 273
                                                ********************99.9******************************************** PP

                                  TIGR01311 274 ekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegv 341
                                                +++++s++gl++t a++++++k+  yalEGsv+++Ga+vqwlrd lk ik++++ve la sveds+gv
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 274 DQCATSHNGLISTAACQVDEQKQ--YALEGSVFIGGAVVQWLRDGLKAIKTSTDVEGLACSVEDSGGV 339
                                                ********************996..******************************************* PP

                                  TIGR01311 342 yfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDG 409
                                                +fVP+f+GL+aPyW+++A+g+ivGl+r++t +hiaraale++afq+ ++l+am +da + +++L+vDG
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 340 VFVPSFTGLGAPYWNPSAKGAIVGLSRGSTVAHIARAALESIAFQSTALLNAMVRDAVSPITELRVDG 407
                                                ******************************************************************** PP

                                  TIGR01311 410 glsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdee 477
                                                g+++nnll+q+qad+lg++v rp+v+ettalGaA++ag+a+gv+++++el++++++e +tfep++ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 408 GAAANNLLLQFQADLLGIPVIRPQVTETTALGAAYLAGIATGVYRDLSELSSQWRME-HTFEPSIGRD 474
                                                ********************************************************7.********** PP

                                  TIGR01311 478 erekkykkwkeaver 492
                                                + +++++ w++a+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS04875 475 QAQARIHAWEAAIRQ 489
                                                ************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (495 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: 9.47
//
[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