Alignments for a candidate for glpK in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Rhodococcus qingshengii djl-6-2

Align glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_076949000.1 C1M55_RS10610 glycerol kinase GlpK

Query= BRENDA::D0VZG4
         (505 letters)



>NCBI__GCF_002893965.1:WP_076949000.1
          Length = 496

 Score =  736 bits (1900), Expect = 0.0
 Identities = 348/498 (69%), Positives = 412/498 (82%), Gaps = 4/498 (0%)

Query: 1   MADYVLAIDQGTTSSRAIVFNHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVG 60
           M  Y+ AIDQGTTSSR ++F+H G + S  Q EH+QIFPRAGWVEH+P  +W N REVV 
Sbjct: 1   MNQYIAAIDQGTTSSRCMIFDHDGAVVSVAQKEHEQIFPRAGWVEHDPVALWINTREVVA 60

Query: 61  LALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGA 120
            AL + +LT  DIAAVGITNQRET VVW+++TGKP+YNAIVWQDTRT ++  ELGGDEG 
Sbjct: 61  GALAKVDLTRADIAAVGITNQRETTVVWERSTGKPIYNAIVWQDTRTDQLCVELGGDEGP 120

Query: 121 EKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGV 180
           +KY+   GLPL+TYF+GPKI+WILDNV+GA+ KAE G+L FG  DTW++WN+T G    V
Sbjct: 121 DKYRDKTGLPLSTYFAGPKIRWILDNVDGAKAKAEAGELCFGTVDTWIVWNLTEG----V 176

Query: 181 HVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSEVYGHGRPRGLVPGVPI 240
           HVTDVTNASRTMLMDL+TL W E I AD GIP+SMLP+IRSSSEVYG GRPRG + GVP+
Sbjct: 177 HVTDVTNASRTMLMDLETLQWDESICADFGIPMSMLPEIRSSSEVYGTGRPRGNLAGVPV 236

Query: 241 AGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIGDAPA 300
           AGILGDQQAATFGQAC   G+AKNTYGTGNF+LLNTGT+ V SK+GLLTTVCYK+G+APA
Sbjct: 237 AGILGDQQAATFGQACLSEGEAKNTYGTGNFMLLNTGTKPVHSKHGLLTTVCYKLGEAPA 296

Query: 301 VYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAPYWRP 360
           VYALEGS+AVTGSLVQWLRDNLG+ ++A D+E LA  V DNGGAYFVPAFSGLFAP WRP
Sbjct: 297 VYALEGSVAVTGSLVQWLRDNLGIIQNAKDIEPLAASVDDNGGAYFVPAFSGLFAPRWRP 356

Query: 361 DARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVANELL 420
           DARG +VGLTR+VN+ H+ARAALEATA+Q+REV+DAM ADSGV+L+ L+VDGGMV NE L
Sbjct: 357 DARGVIVGLTRFVNKGHLARAALEATAYQTREVIDAMRADSGVELSALKVDGGMVVNETL 416

Query: 421 MQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSMESGE 480
           MQFQ+D LGV V+RP V ETTALGAAY AG+A+G+W   +D+ +NWA  K W P+M+  E
Sbjct: 417 MQFQSDILGVPVIRPVVNETTALGAAYTAGLAIGYWADTEDIRNNWAVGKTWEPAMDESE 476

Query: 481 RERLYRNWKKAVTKTMEW 498
           R RLY  W KAV +T  W
Sbjct: 477 RSRLYAEWNKAVERTYNW 494


Lambda     K      H
   0.316    0.134    0.408 

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: 970
Number of extensions: 36
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: 505
Length of database: 496
Length adjustment: 34
Effective length of query: 471
Effective length of database: 462
Effective search space:   217602
Effective search space used:   217602
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_076949000.1 C1M55_RS10610 (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.2307663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-232  757.6   0.5   2.6e-232  757.4   0.5    1.0  1  NCBI__GCF_002893965.1:WP_076949000.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_076949000.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  757.4   0.5  2.6e-232  2.6e-232       1     496 []       3     494 ..       3     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 757.4 bits;  conditional E-value: 2.6e-232
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           ++iaaiDqGttssr+++fd++g +v+ aqke++qifp++gwvEhdp  ++ ++++v+a al+k++ + ++iaa
  NCBI__GCF_002893965.1:WP_076949000.1   3 QYIAAIDQGTTSSRCMIFDHDGAVVSVAQKEHEQIFPRAGWVEHDPVALWINTREVVAGALAKVDLTRADIAA 75 
                                           69*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           +GitnqREttvvW+++tgkp++naivWqdtrt +++ el  +   ++ r+ktGLplstYf++ K+rW+ldnv+
  NCBI__GCF_002893965.1:WP_076949000.1  76 VGITNQRETTVVWERSTGKPIYNAIVWQDTRTDQLCVELGGDEGPDKYRDKTGLPLSTYFAGPKIRWILDNVD 148
                                           ************************************************************************* PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219
                                           +++++ae+gel+fGtvdtw++++Lt+ +vhvtdvtNASRt+l++letl+wde++++ f+ip+++lPeirssse
  NCBI__GCF_002893965.1:WP_076949000.1 149 GAKAKAEAGELCFGTVDTWIVWNLTE-GVHVTDVTNASRTMLMDLETLQWDESICADFGIPMSMLPEIRSSSE 220
                                           *************************7.8********************************************* PP

                             TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292
                                           vyg+ +++    ++vp++g+lGdqqaa +gq+cl++geaKntYgtG+F+llntG+k+v+skhglLttv+yklg
  NCBI__GCF_002893965.1:WP_076949000.1 221 VYGTGRPR-GNLAGVPVAGILGDQQAATFGQACLSEGEAKNTYGTGNFMLLNTGTKPVHSKHGLLTTVCYKLG 292
                                           *****999.8999***********************************************************9 PP

                             TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365
                                           +   ++yalEGsvav+G++vqwlrdnl++i++a+++e+la sv+d++g yfVPafsGLfaP W++dArg+ivG
  NCBI__GCF_002893965.1:WP_076949000.1 293 EAP-AVYALEGSVAVTGSLVQWLRDNLGIIQNAKDIEPLAASVDDNGGAYFVPAFSGLFAPRWRPDARGVIVG 364
                                           755.6******************************************************************** PP

                             TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                           ltr+++k h+araalea a+q+r++++am++d+gve+++LkvDGg++ n++lmq+q+dilgv+v rp v+ett
  NCBI__GCF_002893965.1:WP_076949000.1 365 LTRFVNKGHLARAALEATAYQTREVIDAMRADSGVELSALKVDGGMVVNETLMQFQSDILGVPVIRPVVNETT 437
                                           ************************************************************************* PP

                             TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           alGaA++agla+g+w ++e++++++++  kt+ep+mde+er++ y++w++aver+++w
  NCBI__GCF_002893965.1:WP_076949000.1 438 ALGAAYTAGLAIGYWADTEDIRNNWAVG-KTWEPAMDESERSRLYAEWNKAVERTYNW 494
                                           ***************************7.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (496 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: 32.00
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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