Alignments for a candidate for glpK in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Desulfovibrio vulgaris Miyazaki F

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate 8500046 DvMF_0809 glycerol kinase (RefSeq)

Query= SwissProt::O66131
         (496 letters)



>FitnessBrowser__Miya:8500046
          Length = 497

 Score =  632 bits (1631), Expect = 0.0
 Identities = 307/495 (62%), Positives = 378/495 (76%), Gaps = 1/495 (0%)

Query: 1   MNQYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIA 60
           M +Y+LA+DQGTTSSRAILF+++G+I+ ++QKEFTQ +PQPGWVEHNANEI+ +    + 
Sbjct: 1   MTKYVLALDQGTTSSRAILFSREGDIIQISQKEFTQIYPQPGWVEHNANEIFDTESWGMR 60

Query: 61  SVLSEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYD 120
             L +A +   QV   GITNQRETTVVW+K +G P+YNAIVWQ R+TAG CDELKA+G  
Sbjct: 61  DCLKQAGIDGSQVVAAGITNQRETTVVWDKASGAPVYNAIVWQDRRTAGFCDELKARGLA 120

Query: 121 PLFRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVT 180
             FR+KTGL++DAYFSGTKV+WIL++V GAR +AE+GELLFGTIDTWLIW L+ G+VH T
Sbjct: 121 DTFRQKTGLVLDAYFSGTKVRWILENVPGARAKAEKGELLFGTIDTWLIWNLTKGKVHAT 180

Query: 181 DYSNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAG 240
           D SNASRTL+FNI+T +WDDELL ILGVP++MLP V  SSEV  +  P  F G  +PIAG
Sbjct: 181 DESNASRTLLFNINTGQWDDELLGILGVPRSMLPTVTRSSEVVGEIHP-EFLGKAIPIAG 239

Query: 241 AAGDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYA 300
            AGDQQAA +G AC   GMAKNTYGTGCFMLMNTG++  ASK+ LLTT+AW       +A
Sbjct: 240 NAGDQQAATYGNACLKPGMAKNTYGTGCFMLMNTGKEVHASKNNLLTTMAWATPSGRYFA 299

Query: 301 LEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVR 360
           LEGS+F+AG+ +QWLRDGL +IK A + E  A  V    GVY+VPAF GLG P+WD   R
Sbjct: 300 LEGSVFIAGAVVQWLRDGLGIIKDAPEVEQLALSVPDNGGVYLVPAFAGLGAPHWDQYAR 359

Query: 361 GAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQF 420
           G + G+TRG+TK H  RA LES+A QT D++  M+ D+GI L  LR DGGA +NN LMQF
Sbjct: 360 GTMVGITRGSTKAHIARAALESIALQTLDIMDCMQKDAGIKLAALRADGGATRNNLLMQF 419

Query: 421 QSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTM 480
           Q+D+L VPVERP V ETTALGAAYLAGLAVG+W S ++I A WQL+RRFEP M  + R  
Sbjct: 420 QADVLGVPVERPKVTETTALGAAYLAGLAVGFWKSEEEIEAMWQLDRRFEPNMSAETREK 479

Query: 481 LYDGWKKAVRAAMAF 495
           L   W++AV  A A+
Sbjct: 480 LVYDWQRAVERAKAW 494


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: 805
Number of extensions: 30
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: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
Effective search space:   213906
Effective search space used:   213906
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 8500046 DvMF_0809 (glycerol kinase (RefSeq))
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.30978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-225  735.0   0.9   1.9e-225  734.8   0.9    1.0  1  lcl|FitnessBrowser__Miya:8500046  DvMF_0809 glycerol kinase (RefSe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500046  DvMF_0809 glycerol kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.8   0.9  1.9e-225  1.9e-225       1     496 []       3     494 ..       3     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 734.8 bits;  conditional E-value: 1.9e-225
                         TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGit 77 
                                       k+++a+DqGttssrai+f++eg+++ ++qke++qi+p++gwvEh+++ei+++    +++ l++++i+ ++++a Git
  lcl|FitnessBrowser__Miya:8500046   3 KYVLALDQGTTSSRAILFSREGDIIQISQKEFTQIYPQPGWVEHNANEIFDTESWGMRDCLKQAGIDGSQVVAAGIT 79 
                                       69*************************************************************************** PP

                         TIGR01311  78 nqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaee 154
                                       nqREttvvWdk++g p++naivWqd+rta +++elk+++  +++r+ktGL+l++Yfs+tK+rW+l+nv+++r++ae+
  lcl|FitnessBrowser__Miya:8500046  80 NQRETTVVWDKASGAPVYNAIVWQDRRTAGFCDELKARGLADTFRQKTGLVLDAYFSGTKVRWILENVPGARAKAEK 156
                                       ***************************************************************************** PP

                         TIGR01311 155 gellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekellk 231
                                       gellfGt+dtwli++Lt+gkvh+td +NASRtll+n++t +wd+ell ++++p+++lP+++ ssev+gei+++ +l+
  lcl|FitnessBrowser__Miya:8500046 157 GELLFGTIDTWLIWNLTKGKVHATDESNASRTLLFNINTGQWDDELLGILGVPRSMLPTVTRSSEVVGEIHPE-FLG 232
                                       *************************************************************************.*** PP

                         TIGR01311 232 eevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvava 308
                                       +++pi+g +Gdqqaa +g++clk+g+aKntYgtGcF+l+ntG+++  sk++lLtt+a+ + + +  ++alEGsv++a
  lcl|FitnessBrowser__Miya:8500046 233 KAIPIAGNAGDQQAATYGNACLKPGMAKNTYGTGCFMLMNTGKEVHASKNNLLTTMAWATPSGR--YFALEGSVFIA 307
                                       **********************************************************998665..7********** PP

                         TIGR01311 309 GaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavaf 385
                                       Ga+vqwlrd l++ik+a eve+la sv+d++gvy+VPaf+GL+aP+Wd+ Argt+vG+tr++tk+hiaraale++a+
  lcl|FitnessBrowser__Miya:8500046 308 GAVVQWLRDGLGIIKDAPEVEQLALSVPDNGGVYLVPAFAGLGAPHWDQYARGTMVGITRGSTKAHIARAALESIAL 384
                                       ***************************************************************************** PP

                         TIGR01311 386 qardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleks 462
                                       q+ di+++m+kdag+++++L++DGg+++nnllmq+qad+lgv+verpkv+ettalGaA++aglavg+wkseee+e+ 
  lcl|FitnessBrowser__Miya:8500046 385 QTLDIMDCMQKDAGIKLAALRADGGATRNNLLMQFQADVLGVPVERPKVTETTALGAAYLAGLAVGFWKSEEEIEAM 461
                                       ***************************************************************************** PP

                         TIGR01311 463 aeaeektfepemdeeerekkykkwkeaverslkw 496
                                       ++ + ++fep+m++e+rek +  w++aver++ w
  lcl|FitnessBrowser__Miya:8500046 462 WQLD-RRFEPNMSAETREKLVYDWQRAVERAKAW 494
                                       ***8.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (497 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: 00:00:00.03
# Mc/sec: 7.65
//
[ok]

This GapMind analysis is from Sep 17 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