GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpK in Cronobacter universalis NCTC 9529

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate WP_007798050.1 AFK65_RS00625 glycerol kinase GlpK

Query= CharProtDB::CH_121461
         (502 letters)



>NCBI__GCF_001277175.1:WP_007798050.1
          Length = 505

 Score =  957 bits (2473), Expect = 0.0
 Identities = 463/501 (92%), Positives = 489/501 (97%)

Query: 2   TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTL 61
           TEKKYIVALDQGTTSSRAVV+DHDANI+SVSQREFEQIYP+PGWVEHDPMEIWA+QSSTL
Sbjct: 4   TEKKYIVALDQGTTSSRAVVLDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSSTL 63

Query: 62  VEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGL 121
           VE LAKADISSDQIAAIGITNQRET +VWE+ETGKPI+NAIVWQCRRT+EICE LKRDG+
Sbjct: 64  VEALAKADISSDQIAAIGITNQRETAVVWERETGKPIHNAIVWQCRRTSEICEKLKRDGM 123

Query: 122 EDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHV 181
           EDY+R  TGLVIDPYFSGTKVKWILDHV+G+RERA+RGELLFGTVDTWLIWKMTQGRVHV
Sbjct: 124 EDYVRQATGLVIDPYFSGTKVKWILDHVDGARERAKRGELLFGTVDTWLIWKMTQGRVHV 183

Query: 182 TDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPIS 241
           TDYTNASRTMLFNIH LDWDD+MLE LDIPR MLP+VR+SSEVYGQTNIGGKGGTRIPI+
Sbjct: 184 TDYTNASRTMLFNIHELDWDDRMLEALDIPRAMLPQVRKSSEVYGQTNIGGKGGTRIPIA 243

Query: 242 GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNY 301
           GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAV S +GLLTTIACGP GEVNY
Sbjct: 244 GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVASTHGLLTTIACGPRGEVNY 303

Query: 302 ALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYA 361
           ALEGAVFMAGASIQWLRDEMKLI+DA+DSEYFATKV++TNGVYVVPAFTGLGAPYWDPYA
Sbjct: 304 ALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPYA 363

Query: 362 RGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ 421
           RGAIFGLTRGVN+NHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ
Sbjct: 364 RGAIFGLTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ 423

Query: 422 FQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERN 481
           FQSDILGTRVERPEVREVTALGAAYLAGLAVG+WQNLDELQEKAVIEREFRPGIETTERN
Sbjct: 424 FQSDILGTRVERPEVREVTALGAAYLAGLAVGYWQNLDELQEKAVIEREFRPGIETTERN 483

Query: 482 YRYAGWKKAVKRAMAWEEHDE 502
           YRY GW+KAVKRAMAWEEHD+
Sbjct: 484 YRYEGWRKAVKRAMAWEEHDK 504


Lambda     K      H
   0.318    0.134    0.404 

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: 977
Number of extensions: 22
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: 502
Length of database: 505
Length adjustment: 34
Effective length of query: 468
Effective length of database: 471
Effective search space:   220428
Effective search space used:   220428
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_007798050.1 AFK65_RS00625 (glycerol kinase GlpK)
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.3433710.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-234  764.6   0.8   1.9e-234  764.4   0.8    1.0  1  NCBI__GCF_001277175.1:WP_007798050.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001277175.1:WP_007798050.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  764.4   0.8  1.9e-234  1.9e-234       1     496 []       7     499 ..       7     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 764.4 bits;  conditional E-value: 1.9e-234
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           k+i+a+DqGttssra+v+d+++++v+ +q+e++qi+p++gwvEhdp+ei++s+ ++l eal+k++i++++iaa
  NCBI__GCF_001277175.1:WP_007798050.1   7 KYIVALDQGTTSSRAVVLDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSSTLVEALAKADISSDQIAA 79 
                                           69*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           iGitnqREt+vvW++etgkp++naivWq++rt++i+e+lk+++ e+++r+ tGL++++Yfs+tK++W+ld+v+
  NCBI__GCF_001277175.1:WP_007798050.1  80 IGITNQRETAVVWERETGKPIHNAIVWQCRRTSEICEKLKRDGMEDYVRQATGLVIDPYFSGTKVKWILDHVD 152
                                           ************************************************************************* PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219
                                           ++r++a++gellfGtvdtwli+k+t+g+vhvtd+tNASRt+l+n+++l+wd+++le+++ip+++lP++r+sse
  NCBI__GCF_001277175.1:WP_007798050.1 153 GARERAKRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHELDWDDRMLEALDIPRAMLPQVRKSSE 225
                                           ************************************************************************* PP

                             TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292
                                           vyg+++     ++++pi+g++Gdqqaal+gqlc+k+g+aKntYgtGcF+l+ntGek+v s+hglLtt+a+   
  NCBI__GCF_001277175.1:WP_007798050.1 226 VYGQTNIGGKGGTRIPIAGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVASTHGLLTTIACGPR 298
                                           ********9*************************************************************999 PP

                             TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365
                                           g+   +yalEG+v++aGa +qwlrd++kli++a ++e +a++v+d++gvy+VPaf+GL+aPyWd+ Arg+i+G
  NCBI__GCF_001277175.1:WP_007798050.1 299 GEV--NYALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPYARGAIFG 369
                                           877..6******************************************************************* PP

                             TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                           ltr+++++hi+ra+le++a+q+rd+leam++d+g+++++L+vDGg+++nn+lmq+q+dilg++verp+v e+t
  NCBI__GCF_001277175.1:WP_007798050.1 370 LTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVT 442
                                           ************************************************************************* PP

                             TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           alGaA++aglavg+w++++el+++a  e ++f+p ++++er+ +y+ w++av+r++ w
  NCBI__GCF_001277175.1:WP_007798050.1 443 ALGAAYLAGLAVGYWQNLDELQEKAVIE-REFRPGIETTERNYRYEGWRKAVKRAMAW 499
                                           ************************9997.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (505 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.56
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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