Alignments for a candidate for glpK in Nocardiopsis baichengensis YIM 90130

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Nocardiopsis baichengensis YIM 90130

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_017557777.1 C892_RS0114335 glycerol kinase GlpK

Query= SwissProt::O66131
         (496 letters)



>NCBI__GCF_000341205.1:WP_017557777.1
          Length = 492

 Score =  477 bits (1228), Expect = e-139
 Identities = 242/486 (49%), Positives = 318/486 (65%), Gaps = 7/486 (1%)

Query: 5   MLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVLS 64
           +L ID GTT   A++  + G ++    +EF Q++P+ GWVEH   EIW + LA   S L 
Sbjct: 3   VLTIDAGTTGVTALMVGEDGRVLSRGYQEFAQHYPEAGWVEHVPEEIWQAALAACQSALD 62

Query: 65  EAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLFR 124
            A   P  V   GITNQRET V+W +  G+    A+VWQ R+TAGIC EL+  G++    
Sbjct: 63  AAGTPPTCV---GITNQRETAVLWNRKRGSSPRRAVVWQDRRTAGICTELREAGHEDRVT 119

Query: 125 KKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYSN 184
           + TGL +D YF+GTK+ WI  +   A    E GE   GT+D+++I +L+GG  HVTD SN
Sbjct: 120 EVTGLRLDPYFTGTKLTWIKRNDQRAWSGVESGETAVGTVDSYIIARLTGGARHVTDASN 179

Query: 185 ASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAGD 244
           ASRTL+++I    W +E+ ++ GVP + LPEV PS     +T P  F G+ +P++G AGD
Sbjct: 180 ASRTLLYDIRRGAWSEEMCELFGVPVSALPEVVPSYGSVGETDPEEFLGLRLPVSGIAGD 239

Query: 245 QQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAW-GIDGKVEYALEG 303
           QQAA+FGQ C+  G +K TYGTG F+L+NTGE+ VA  HGLL+T+ W   DG++EYALEG
Sbjct: 240 QQAAMFGQNCYRPGTSKCTYGTGSFILVNTGEETVAPDHGLLSTVLWQHPDGRLEYALEG 299

Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363
           SIFV G+A+QWLRDGL +I TAA SE  A  V  + GV  VPA  GLG P WD   RGAV
Sbjct: 300 SIFVTGAAVQWLRDGLGLIDTAAQSEGLAASVPDSGGVVFVPALTGLGAPDWDPHARGAV 359

Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQFQSD 423
           FG+TRGT + H  RATL+++A++ +DV   M   SG  +  LRVDGGA  N+ L Q Q+D
Sbjct: 360 FGITRGTGRAHLARATLDAIAFEVRDVAEAMARASGTQVPELRVDGGASANDLLCQIQAD 419

Query: 424 LLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTMLYD 483
            L V V RP V ETTALGAA+LAGL  G W+S D++   W+L+RRFEP   DD +   Y 
Sbjct: 420 QLGVSVARPQVQETTALGAAFLAGLGTGVWSSTDELERTWKLDRRFEPGERDDAQ---YR 476

Query: 484 GWKKAV 489
            W+ AV
Sbjct: 477 RWRTAV 482


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: 747
Number of extensions: 27
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: 496
Length of database: 492
Length adjustment: 34
Effective length of query: 462
Effective length of database: 458
Effective search space:   211596
Effective search space used:   211596
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_017557777.1 C892_RS0114335 (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.1279899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-187  608.9   0.0     3e-187  608.8   0.0    1.0  1  NCBI__GCF_000341205.1:WP_017557777.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341205.1:WP_017557777.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.8   0.0    3e-187    3e-187       3     496 .]       3     488 ..       1     488 [. 0.98

  Alignments for each domain:
  == domain 1  score: 608.8 bits;  conditional E-value: 3e-187
                             TIGR01311   3 iaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiG 75 
                                           +++iD Gtt+  a++  ++g+++++ ++e+ q++p++gwvEh p+ei++++++++++al+++++ +   +++G
  NCBI__GCF_000341205.1:WP_017557777.1   3 VLTIDAGTTGVTALMVGEDGRVLSRGYQEFAQHYPEAGWVEHVPEEIWQAALAACQSALDAAGTPP---TCVG 72 
                                           889**********************************************************99877...69** PP

                             TIGR01311  76 itnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveev 148
                                           itnqREt+v+W+++ g+    a+vWqd+rta i++el+e+++e++++e tGL l++Yf++tKl W+  n +++
  NCBI__GCF_000341205.1:WP_017557777.1  73 ITNQRETAVLWNRKRGSSPRRAVVWQDRRTAGICTELREAGHEDRVTEVTGLRLDPYFTGTKLTWIKRNDQRA 145
                                           ************************************************************************* PP

                             TIGR01311 149 rkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevy 221
                                            + +e+ge  +Gtvd+++i +Ltgg+ hvtd++NASRtll+++++ +w+ee++elf++p + lPe+++s   +
  NCBI__GCF_000341205.1:WP_017557777.1 146 WSGVESGETAVGTVDSYIIARLTGGARHVTDASNASRTLLYDIRRGAWSEEMCELFGVPVSALPEVVPSYGSV 218
                                           ************************************************************************* PP

                             TIGR01311 222 geieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggk 294
                                           ge++++e+l+ ++p++g++Gdqqaa++gq c+++g+ K+tYgtG+F+l+ntGe++v  +hglL+tv ++  + 
  NCBI__GCF_000341205.1:WP_017557777.1 219 GETDPEEFLGLRLPVSGIAGDQQAAMFGQNCYRPGTSKCTYGTGSFILVNTGEETVAPDHGLLSTVLWQHPDG 291
                                           *********************************************************************9776 PP

                             TIGR01311 295 kptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGlt 367
                                           +  +yalEGs++v+Gaavqwlrd l+li++a+++e la sv+ds+gv+fVPa++GL+aP Wd++Arg+++G+t
  NCBI__GCF_000341205.1:WP_017557777.1 292 RL-EYALEGSIFVTGAAVQWLRDGLGLIDTAAQSEGLAASVPDSGGVVFVPALTGLGAPDWDPHARGAVFGIT 363
                                           64.9********************************************************************* PP

                             TIGR01311 368 rkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettal 440
                                           r+t ++h+ara+l+a+af++rd+ eam++ +g++v +L+vDGg+s+n+ll+qiqad lgv+v+rp+v+ettal
  NCBI__GCF_000341205.1:WP_017557777.1 364 RGTGRAHLARATLDAIAFEVRDVAEAMARASGTQVPELRVDGGASANDLLCQIQADQLGVSVARPQVQETTAL 436
                                           ************************************************************************* PP

                             TIGR01311 441 GaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           GaA++agl +gvw+s++ele++++ + ++fep   +   +++y++w++avers++w
  NCBI__GCF_000341205.1:WP_017557777.1 437 GAAFLAGLGTGVWSSTDELERTWKLD-RRFEPGERD---DAQYRRWRTAVERSKGW 488
                                           *************************8.9***97655...678************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (492 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.48
//
[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 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