Alignments for a candidate for glpK in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Stenotrophomonas chelatiphaga DSM 21508

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_057508106.1 ABB28_RS07845 glycerol kinase

Query= SwissProt::O66131
         (496 letters)



>NCBI__GCF_001431535.1:WP_057508106.1
          Length = 496

 Score =  714 bits (1842), Expect = 0.0
 Identities = 339/493 (68%), Positives = 408/493 (82%)

Query: 3   QYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASV 62
           +++LAIDQGTTSSRAILF++ G I   AQ+EF Q FPQPGWVEH+  EI  SV   +  +
Sbjct: 4   EFILAIDQGTTSSRAILFDRDGRIAGSAQREFAQLFPQPGWVEHDPREILTSVYTTLTEL 63

Query: 63  LSEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPL 122
           L++ QV P ++AGIGITNQRETTVVW++ TG PI+NAIVWQSRQ+  IC+ L+A G++ L
Sbjct: 64  LNQQQVDPRRIAGIGITNQRETTVVWDRATGQPIHNAIVWQSRQSQAICERLQADGHEAL 123

Query: 123 FRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDY 182
            R +TGL++DAYFS TK++WILDHVDGA+ RAERGELLFGTID+WLIW L+GG VHVTD 
Sbjct: 124 IRSRTGLVVDAYFSATKIRWILDHVDGAQARAERGELLFGTIDSWLIWNLTGGAVHVTDM 183

Query: 183 SNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAA 242
           +NA+RTL+FNIHTL WDD+LL +L +P+AMLP VR SSEVY  T P  FF  ++PIAG A
Sbjct: 184 TNAARTLLFNIHTLAWDDDLLALLDIPRAMLPHVRGSSEVYGHTRPQFFFDRQIPIAGIA 243

Query: 243 GDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALE 302
           GDQQAALFGQACF  GMAKNTYGTGCFMLMNTG +AVAS +GLLTTIAW +DG+VEYALE
Sbjct: 244 GDQQAALFGQACFEPGMAKNTYGTGCFMLMNTGSQAVASANGLLTTIAWNVDGQVEYALE 303

Query: 303 GSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGA 362
           GSIFVAGS +QWLRDGLRM   ++D + YAE+V  T GVY+VPAF+GLG PYW S+VRGA
Sbjct: 304 GSIFVAGSVVQWLRDGLRMFGKSSDCQAYAERVPDTGGVYLVPAFVGLGAPYWRSDVRGA 363

Query: 363 VFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQFQS 422
           +FG+TRGT+KEHFIRA +ES+AYQT+DVLA M+AD+GI L  LR DGGA+ N+F+ QFQS
Sbjct: 364 MFGVTRGTSKEHFIRAAVESMAYQTRDVLAAMQADAGIELKELRADGGAIANDFMGQFQS 423

Query: 423 DLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTMLY 482
           DLL VPV RP V ETTALGAAYLAGLAVG+W SR  IAAQW ++RRFEP M  D+R  LY
Sbjct: 424 DLLGVPVLRPQVAETTALGAAYLAGLAVGFWESRAQIAAQWGVDRRFEPTMSADRREALY 483

Query: 483 DGWKKAVRAAMAF 495
            GW++AV AA+A+
Sbjct: 484 AGWQRAVNAALAW 496


Lambda     K      H
   0.319    0.134    0.406 

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: 878
Number of extensions: 35
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: 496
Length of database: 496
Length adjustment: 34
Effective length of query: 462
Effective length of database: 462
Effective search space:   213444
Effective search space used:   213444
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 WP_057508106.1 ABB28_RS07845 (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.21038.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-226  737.2   0.1   3.8e-226  737.1   0.1    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508106.1  ABB28_RS07845 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508106.1  ABB28_RS07845 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.1   0.1  3.8e-226  3.8e-226       2     496 .]       5     496 .]       4     496 .] 0.99

  Alignments for each domain:
  == domain 1  score: 737.1 bits;  conditional E-value: 3.8e-226
                                 TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                               +i+aiDqGttssrai+fd++g++ ++aq+e+ q fp++gwvEhdp eil+sv ++l+e l++ +++++ 
  lcl|NCBI__GCF_001431535.1:WP_057508106.1   5 FILAIDQGTTSSRAILFDRDGRIAGSAQREFAQLFPQPGWVEHDPREILTSVYTTLTELLNQQQVDPRR 73 
                                               8******************************************************************** PP

                                 TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139
                                               ia iGitnqREttvvWd++tg+p++naivWq+++ + i+e+l+++++e  +r++tGL++++YfsatK+r
  lcl|NCBI__GCF_001431535.1:WP_057508106.1  74 IAGIGITNQRETTVVWDRATGQPIHNAIVWQSRQSQAICERLQADGHEALIRSRTGLVVDAYFSATKIR 142
                                               ********************************************************************* PP

                                 TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208
                                               W+ld+v++++++ae+gellfGt+d+wli++Ltgg+vhvtd+tNA+Rtll+n++tl+wd++ll+l++ip+
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 143 WILDHVDGAQARAERGELLFGTIDSWLIWNLTGGAVHVTDMTNAARTLLFNIHTLAWDDDLLALLDIPR 211
                                               ********************************************************************* PP

                                 TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277
                                               ++lP++r ssevyg+++++ ++ +++pi+g++Gdqqaal+gq+c+++g+aKntYgtGcF+l+ntG+++v
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 212 AMLPHVRGSSEVYGHTRPQFFFDRQIPIAGIAGDQQAALFGQACFEPGMAKNTYGTGCFMLMNTGSQAV 280
                                               ********************************************************************* PP

                                 TIGR01311 278 iskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPa 346
                                                s +glLtt+a++++g+    yalEGs++vaG++vqwlrd l+++ k+++++++a++v+d++gvy+VPa
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 281 ASANGLLTTIAWNVDGQVE--YALEGSIFVAGSVVQWLRDGLRMFGKSSDCQAYAERVPDTGGVYLVPA 347
                                               ****************985..************************************************ PP

                                 TIGR01311 347 fsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknn 415
                                               f GL+aPyW+sd rg+++G+tr+t keh++raa+e++a+q+rd+l+am++dag+e+k+L++DGg+++n+
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 348 FVGLGAPYWRSDVRGAMFGVTRGTSKEHFIRAAVESMAYQTRDVLAAMQADAGIELKELRADGGAIAND 416
                                               ********************************************************************* PP

                                 TIGR01311 416 llmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkyk 484
                                               ++ q+q+d+lgv+v rp+vaettalGaA++aglavg+w+s  ++++++ ++ ++fep+m++++re+ y+
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 417 FMGQFQSDLLGVPVLRPQVAETTALGAAYLAGLAVGFWESRAQIAAQWGVD-RRFEPTMSADRREALYA 484
                                               **************************************************8.***************** PP

                                 TIGR01311 485 kwkeaverslkw 496
                                                w++av+ +l w
  lcl|NCBI__GCF_001431535.1:WP_057508106.1 485 GWQRAVNAALAW 496
                                               *******99887 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 12.63
//
[ok]

This GapMind analysis is from Sep 24 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