GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Herbaspirillum seropedicae SmR1

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate HSERO_RS17870 HSERO_RS17870 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__HerbieS:HSERO_RS17870
          Length = 333

 Score =  245 bits (625), Expect = 1e-69
 Identities = 133/313 (42%), Positives = 175/313 (55%), Gaps = 2/313 (0%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLE-EHKVEVKDGCIAIA 64
           L+ D+GGTNAR AL +   G I Q +   G DY      ++ YL+      V+   +AIA
Sbjct: 18  LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGHPPVRHAVVAIA 76

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            P+ GD + MTNH WAFSI   ++ LGF  L ++NDFTA+SMA+P L+ + L Q GG  P
Sbjct: 77  NPVQGDQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAP 136

Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184
             G PI + GAGTGLGV  L+H D  W+ L  EGGH  FAP    EA +L        HV
Sbjct: 137 KPGAPIGLVGAGTGLGVGGLLHADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHV 196

Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244
           SAER++SGPGL  ++RA++  D      L    I E A       C+  L+LFC ++G  
Sbjct: 197 SAERLVSGPGLELIHRALLAIDGHPAAELSAAQIVEGARQHGDALCQETLALFCSMLGTV 256

Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304
             +LAL LG  GG++I  G+VP   ++F  S FRA FE+KGR       IP Y+I  + P
Sbjct: 257 AADLALTLGALGGIYIGVGVVPHLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYP 316

Query: 305 GLLGSGAHLRQTL 317
              G  A L   L
Sbjct: 317 AFTGVSAILADRL 329


Lambda     K      H
   0.322    0.141    0.426 

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: 358
Number of extensions: 15
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: 321
Length of database: 333
Length adjustment: 28
Effective length of query: 293
Effective length of database: 305
Effective search space:    89365
Effective search space used:    89365
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate HSERO_RS17870 HSERO_RS17870 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

# 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/TIGR00749.hmm
# target sequence database:        /tmp/gapView.5544.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00749  [M=315]
Accession:   TIGR00749
Description: glk: glucokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    8.4e-97  310.2   0.0    9.8e-97  309.9   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17870  HSERO_RS17870 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17870  HSERO_RS17870 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.9   0.0   9.8e-97   9.8e-97       1     313 [.      18     320 ..      18     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 309.9 bits;  conditional E-value: 9.8e-97
                                  TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaiatPiig 67 
                                                l++diGGtnar+al e  pg+ieqv+++++ d+ +++++v+ yl+ a      p+ ++ +aia P+ g
  lcl|FitnessBrowser__HerbieS:HSERO_RS17870  18 LLADIGGTNARFAL-ETGPGRIEQVQILRGADYGEFTDAVQAYLKLAGH---PPVrHAVVAIANPVQG 81 
                                                79************.****************************987654...466579********** PP

                                  TIGR00749  68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGt 135
                                                d +++tn+dWa+sie  +q l+++ l ++ndf+a ++a++ l+ ++l q+gg  ++++a+i ++GaGt
  lcl|FitnessBrowser__HerbieS:HSERO_RS17870  82 DQIKMTNHDWAFSIEAARQLLGFELLLVVNDFTALSMAVPQLRADELQQVGGGAPKPGAPIGLVGAGT 149
                                                ******************************************************************** PP

                                  TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealsk 203
                                                GlGv  l++ +dg++  la+eGgh+ faP ++ e+ +l y+ +  ++vsaer++sG+Gl li++al  
  lcl|FitnessBrowser__HerbieS:HSERO_RS17870 150 GLGVGGLLH-ADGHWLPLASEGGHAAFAPADPREAAVLAYAWQFHEHVSAERLVSGPGLELIHRALLA 216
                                                *********.*********************************************************9 PP

                                  TIGR00749 204 rkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivP 271
                                                 +g+      + +el   +i e a +  d+l++++l lf+s+lG++a++lal+lga GG+y+  G+vP
  lcl|FitnessBrowser__HerbieS:HSERO_RS17870 217 IDGH------PAAELSAAQIVEGARQHGDALCQETLALFCSMLGTVAADLALTLGALGGIYIGVGVVP 278
                                                9953......45666788899*********************************************** PP

                                  TIGR00749 272 rfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313
                                                ++ +++ +s+fra+fe+kGr+  l + iP +v+  + + + G
  lcl|FitnessBrowser__HerbieS:HSERO_RS17870 279 HLGDYFARSPFRARFENKGRMSVLTKAIPTYVITAEYPAFTG 320
                                                *********************************999988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (333 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: 7.58
//
[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:

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:

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:

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:

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