Alignments for a candidate for glpK in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate Echvi_1770 Echvi_1770 glycerol kinase

Query= SwissProt::Q9WX53
         (496 letters)



>FitnessBrowser__Cola:Echvi_1770
          Length = 500

 Score =  619 bits (1597), Expect = 0.0
 Identities = 292/488 (59%), Positives = 370/488 (75%), Gaps = 1/488 (0%)

Query: 3   QYILAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASV 62
           Q+I+A+DQGTTSSRAILF+Q G+ + +AQK+F Q+FP+ GWVEH+A EIW S  AVI   
Sbjct: 6   QFIMALDQGTTSSRAILFDQSGQSIAIAQKDFKQHFPKAGWVEHDAKEIWTSQAAVILEA 65

Query: 63  LSEAQVKPEQVAGIGITNQRETTVVWVKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPL 122
           +++A+++P QVAGIGITNQRETT++W + +G P+Y AIVWQ R+T+  C+ LK +GY  +
Sbjct: 66  IAQAEIEPGQVAGIGITNQRETTILWDRKSGKPLYRAIVWQDRRTSAYCNRLKREGYRDM 125

Query: 123 FREKTGLLIDAYFSGTKVKWILDHVEGARERAERGELLFGTIDTWLIWKLSGGRAHVTDY 182
             +KTGL+IDAYFS TK+KWILD+VEG RE+AE+GE+ FGT+D+WL+WKL+ G+ H+TD 
Sbjct: 126 INQKTGLIIDAYFSATKIKWILDNVEGVREKAEKGEVCFGTVDSWLVWKLTNGQQHLTDI 185

Query: 183 SNASRTLMFNIHTLEWDDELLAILNVPKAMLPEVRPSSEVYAKTVPHHFFGVEVPIAGAA 242
           +NASRT++FNIH  +WD+ELL + ++PK++LPEVR SSEVY  T     F  ++PI G A
Sbjct: 186 TNASRTMLFNIHDKQWDEELLELFDIPKSILPEVRSSSEVYCTTAGD-IFSAKIPIGGIA 244

Query: 243 GDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVQSKHGLLTTIAWGIDGKVEYALE 302
           GDQQAALFGQ C   GM K TYGTGCFM+MNTGEK VQS + LLTTIAW + GKV YALE
Sbjct: 245 GDQQAALFGQRCTQPGMVKTTYGTGCFMVMNTGEKPVQSSNQLLTTIAWEVAGKVHYALE 304

Query: 303 GSIFVAGSAIQWLRDGLRMIKTAADSEAYAEKVESTDGVYVVPAFVGLGTPYWDSEVRGA 362
           GS+F+ G+AIQWLRDGL + + A  SE+ A  VE   GVY VPA  GLG PYWD + RGA
Sbjct: 305 GSVFIGGAAIQWLRDGLAIFEEAEQSESLATSVEDNGGVYFVPALTGLGAPYWDQDARGA 364

Query: 363 VFGLTRGTTKEHFIRATLESLAYQTKDVLAAMEADSGISLTTLRVDGGAVKNNFLMQFQS 422
            FG+TRGTT+ HF RA LE++A+Q  DVLAAME D+G     +RVDGGA  NNFLMQFQ+
Sbjct: 365 FFGITRGTTQAHFARAALEAIAFQVFDVLAAMEKDAGAKTKEMRVDGGASANNFLMQFQA 424

Query: 423 DLLAVPVERPVINETTALGAPYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTMLY 482
           DLL   V+RP I ETTALGA +LAGLAVGYW  + ++   W+ E  F PK D +    L 
Sbjct: 425 DLLRSEVKRPQITETTALGAAFLAGLAVGYWKDQTELQQLWKEEASFPPKSDRNVTDELL 484

Query: 483 DGWKKAVR 490
             W KAV+
Sbjct: 485 HFWHKAVQ 492


Lambda     K      H
   0.319    0.134    0.405 

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: 796
Number of extensions: 26
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: 500
Length adjustment: 34
Effective length of query: 462
Effective length of database: 466
Effective search space:   215292
Effective search space used:   215292
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 Echvi_1770 Echvi_1770 (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.18795.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.7e-231  753.6   4.7   4.2e-231  753.4   4.7    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1770  Echvi_1770 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1770  Echvi_1770 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  753.4   4.7  4.2e-231  4.2e-231       1     496 []       6     497 ..       6     497 .. 0.99

  Alignments for each domain:
  == domain 1  score: 753.4 bits;  conditional E-value: 4.2e-231
                            TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                          ++i+a+DqGttssrai+fd++g+ +a+aqk+++q+fpk+gwvEhd++ei++s+ +v+ ea++++ei++ ++a i
  lcl|FitnessBrowser__Cola:Echvi_1770   6 QFIMALDQGTTSSRAILFDQSGQSIAIAQKDFKQHFPKAGWVEHDAKEIWTSQAAVILEAIAQAEIEPGQVAGI 79 
                                          69************************************************************************ PP

                            TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveev 148
                                          GitnqREtt++Wd+++gkpl+ aivWqd+rt+ ++++lk+e++ +++++ktGL++++YfsatK++W+ldnve+v
  lcl|FitnessBrowser__Cola:Echvi_1770  80 GITNQRETTILWDRKSGKPLYRAIVWQDRRTSAYCNRLKREGYRDMINQKTGLIIDAYFSATKIKWILDNVEGV 153
                                          ************************************************************************** PP

                            TIGR01311 149 rkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevyg 222
                                          r++ae+ge++fGtvd+wl++kLt+g++h+td+tNASRt+l+n+++++wdeellelf+ipk++lPe+rsssevy+
  lcl|FitnessBrowser__Cola:Echvi_1770 154 REKAEKGEVCFGTVDSWLVWKLTNGQQHLTDITNASRTMLFNIHDKQWDEELLELFDIPKSILPEVRSSSEVYC 227
                                          ************************************************************************** PP

                            TIGR01311 223 eieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkp 296
                                          +++ + ++ +++pi g++Gdqqaal+gq c+++g++K+tYgtGcF+++ntGek+v s+++lLtt+a+++ gk  
  lcl|FitnessBrowser__Cola:Echvi_1770 228 TTAGD-IFSAKIPIGGIAGDQQAALFGQRCTQPGMVKTTYGTGCFMVMNTGEKPVQSSNQLLTTIAWEVAGKV- 299
                                          *9998.****************************************************************987. PP

                            TIGR01311 297 tkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkt 370
                                           +yalEGsv+++Gaa+qwlrd l ++++ae++e+la+sved++gvyfVPa++GL+aPyWd+dArg+++G+tr+t
  lcl|FitnessBrowser__Cola:Echvi_1770 300 -HYALEGSVFIGGAAIQWLRDGLAIFEEAEQSESLATSVEDNGGVYFVPALTGLGAPYWDQDARGAFFGITRGT 372
                                          .6************************************************************************ PP

                            TIGR01311 371 tkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAl 444
                                          t++h+araalea+afq+ d+l+amekdag+++k+++vDGg+s+nn+lmq+qad+l  +v+rp+++ettalGaA+
  lcl|FitnessBrowser__Cola:Echvi_1770 373 TQAHFARAALEAIAFQVFDVLAAMEKDAGAKTKEMRVDGGASANNFLMQFQADLLRSEVKRPQITETTALGAAF 446
                                          ************************************************************************** PP

                            TIGR01311 445 aaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                          +aglavg+wk+++el++ +++e  +f p++d++  ++ ++ w++av+rs++w
  lcl|FitnessBrowser__Cola:Echvi_1770 447 LAGLAVGYWKDQTELQQLWKEE-ASFPPKSDRNVTDELLHFWHKAVQRSKDW 497
                                          ********************97.***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (500 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: 9.77
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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