Alignments for a candidate for glk in Herbaspirillum seropedicae SmR1

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.2847.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: 7.92
//
[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