Alignments for a candidate for glpK in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Derxia gummosa DSM 723

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate WP_028311075.1 H566_RS0108280 glycerol kinase

Query= CharProtDB::CH_121461
         (502 letters)



>NCBI__GCF_000482785.1:WP_028311075.1
          Length = 489

 Score =  482 bits (1240), Expect = e-140
 Identities = 249/490 (50%), Positives = 320/490 (65%), Gaps = 6/490 (1%)

Query: 8   VALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAK 67
           +ALDQG++SSRA V D D +  +V Q+     +P+PGWVEHDP EIW TQ     + L  
Sbjct: 5   LALDQGSSSSRAAVFDTDGHHTAVVQKPLPVRFPRPGWVEHDPAEIWHTQLDAARDALLA 64

Query: 68  ADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRS 127
              ++ +++ I ITNQRETT+VW + +G PI  AI WQ RRT + CE  + +GL   +R 
Sbjct: 65  GGSATLELSGIAITNQRETTLVWSRRSGAPIGPAISWQDRRTVDWCEARRAEGLAPLVRE 124

Query: 128 NTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNA 187
            TGLVIDPYFS  K+ W+LDH+ G+R+ A  GEL FGTVD+WLIWK+T G VH TD TNA
Sbjct: 125 RTGLVIDPYFSAGKIAWLLDHLPGARQLAEAGELAFGTVDSWLIWKLTNGAVHATDVTNA 184

Query: 188 SRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAGDQ 247
           SRTMLFN+    WD ++ E L IP  +LP+V+ S+  YG   +    G  + I G+AGDQ
Sbjct: 185 SRTMLFNLERGAWDPELCERLRIPMALLPQVKPSASYYGDCEV---LGGNVSIMGVAGDQ 241

Query: 248 QAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAV 307
           QAALFG  C+  G AKNTYGTGCF+L++TGE+AV S++GLLTT A   +    YALEGAV
Sbjct: 242 QAALFGHGCLLPGQAKNTYGTGCFVLLHTGEEAVASKHGLLTTRAAQISRLKEYALEGAV 301

Query: 308 FMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFG 367
           F AG+ +QWLRDE++L     D E  A  V +T GV +VPAF GLG+PYWDP AR  + G
Sbjct: 302 FDAGSVVQWLRDEVRLFTRTADIEPLAASVPDTGGVVLVPAFNGLGSPYWDPSARAGLLG 361

Query: 368 LTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDIL 427
           +TRG +  HI RA LESIA Q+ +VL AMQAD+  +L  L VDGGA ANN LMQ Q+D+L
Sbjct: 362 MTRGTSRAHIARAALESIALQSTEVLLAMQADAATKLTELVVDGGASANNLLMQMQADLL 421

Query: 428 GTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGW 487
           G  V RP   E TA GAA +A    G +Q+ +     + +   F+P +   E   R   W
Sbjct: 422 GVPVRRPANIEATAFGAASIAAHTTGTFQHAENQDLDSTV---FQPVMSRDEAAARLDRW 478

Query: 488 KKAVKRAMAW 497
           + AV R   W
Sbjct: 479 RMAVGRVGGW 488


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: 685
Number of extensions: 23
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: 502
Length of database: 489
Length adjustment: 34
Effective length of query: 468
Effective length of database: 455
Effective search space:   212940
Effective search space used:   212940
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_028311075.1 H566_RS0108280 (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.1174496.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-193  627.8   0.0   6.1e-193  627.5   0.0    1.0  1  NCBI__GCF_000482785.1:WP_028311075.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028311075.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.5   0.0  6.1e-193  6.1e-193       4     496 .]       5     488 ..       3     488 .. 0.98

  Alignments for each domain:
  == domain 1  score: 627.5 bits;  conditional E-value: 6.1e-193
                             TIGR01311   4 aaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGi 76 
                                           +a+DqG +ssra vfd++g++ a  qk l   fp++gwvEhdp ei+++++ ++++al + +  + e++ i i
  NCBI__GCF_000482785.1:WP_028311075.1   5 LALDQGSSSSRAAVFDTDGHHTAVVQKPLPVRFPRPGWVEHDPAEIWHTQLDAARDALLAGGSATLELSGIAI 77 
                                           69*********************************************************************** PP

                             TIGR01311  77 tnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevr 149
                                           tnqREtt+vW++++g p+ +ai Wqd+rt + +e+ ++e+    +re+tGL++++Yfsa K++Wlld+ +++r
  NCBI__GCF_000482785.1:WP_028311075.1  78 TNQRETTLVWSRRSGAPIGPAISWQDRRTVDWCEARRAEGLAPLVRERTGLVIDPYFSAGKIAWLLDHLPGAR 150
                                           ************************************************************************* PP

                             TIGR01311 150 kaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevyg 222
                                           + ae+gel fGtvd+wli+kLt+g+vh+tdvtNASRt+l+nle+ +wd el+e ++ip++llP++++s+++yg
  NCBI__GCF_000482785.1:WP_028311075.1 151 QLAEAGELAFGTVDSWLIWKLTNGAVHATDVTNASRTMLFNLERGAWDPELCERLRIPMALLPQVKPSASYYG 223
                                           ************************************************************************* PP

                             TIGR01311 223 eieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkk 295
                                           ++e   +l+ +v i+gv+Gdqqaal+g+ cl +g+aKntYgtGcF+ll+tGe++v skhglLtt a ++++ k
  NCBI__GCF_000482785.1:WP_028311075.1 224 DCE---VLGGNVSIMGVAGDQQAALFGHGCLLPGQAKNTYGTGCFVLLHTGEEAVASKHGLLTTRAAQISRLK 293
                                           997...57**************************************************************988 PP

                             TIGR01311 296 ptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltr 368
                                              yalEG+v+ aG++vqwlrd+++l+++++++e+la sv+d++gv++VPaf+GL++PyWd++Ar+ ++G+tr
  NCBI__GCF_000482785.1:WP_028311075.1 294 E--YALEGAVFDAGSVVQWLRDEVRLFTRTADIEPLAASVPDTGGVVLVPAFNGLGSPYWDPSARAGLLGMTR 364
                                           5..********************************************************************** PP

                             TIGR01311 369 kttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalG 441
                                           +t ++hiaraale++a+q+ ++l am++da +++++L vDGg+s+nnllmq+qad+lgv+v+rp + e+ta+G
  NCBI__GCF_000482785.1:WP_028311075.1 365 GTSRAHIARAALESIALQSTEVLLAMQADAATKLTELVVDGGASANNLLMQMQADLLGVPVRRPANIEATAFG 437
                                           ************************************************************************* PP

                             TIGR01311 442 aAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           aA +a+ ++g++++ e+    +    ++f+p m+++e ++++ +w+ av r  +w
  NCBI__GCF_000482785.1:WP_028311075.1 438 AASIAAHTTGTFQHAENQDLDS----TVFQPVMSRDEAAARLDRWRMAVGRVGGW 488
                                           **********888666554433....57*********************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (489 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.12
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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