Alignments for a candidate for glpK in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Shewanella oneidensis MR-1

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate 203312 SO4230 glycerol kinase (NCBI ptt file)

Query= CharProtDB::CH_121461
         (502 letters)



>FitnessBrowser__MR1:203312
          Length = 494

 Score =  746 bits (1927), Expect = 0.0
 Identities = 355/491 (72%), Positives = 417/491 (84%), Gaps = 1/491 (0%)

Query: 3   EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLV 62
           +KKY+VALDQGTTSSRA+V DHDANI+SVSQREF Q+YP PGWVEHDPMEIWA+QSS L+
Sbjct: 2   QKKYVVALDQGTTSSRAIVFDHDANIVSVSQREFTQLYPNPGWVEHDPMEIWASQSSVLI 61

Query: 63  EVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLE 122
           E LA+A I SD +AAIGITNQRETTI+WEK TGKP+YNAIVWQCRR+AEICE LK  GLE
Sbjct: 62  ESLARAGIHSDAVAAIGITNQRETTIIWEKATGKPVYNAIVWQCRRSAEICEQLKAQGLE 121

Query: 123 DYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVT 182
           DY+R NTGL++DPYFSGTK+KWILD+V  +R +A+RGELLFGTVDTWL+WK+T+G+VHVT
Sbjct: 122 DYVRQNTGLLLDPYFSGTKIKWILDNVPDARAKAKRGELLFGTVDTWLLWKLTEGKVHVT 181

Query: 183 DYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISG 242
           D TNA+RT+LFNIH+L WD K+LE LDIP  MLPEV+ S  VYG T I G+ G+ IP++G
Sbjct: 182 DPTNAARTLLFNIHSLSWDSKLLEALDIPAAMLPEVKPSCSVYGTTRIAGE-GSEIPLAG 240

Query: 243 IAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYA 302
           IAGDQQAALFGQLCV++GMAKNTYGTGCF+LMNTG KAV+S +GLLTT+A G  GEVNYA
Sbjct: 241 IAGDQQAALFGQLCVEQGMAKNTYGTGCFLLMNTGSKAVRSSHGLLTTVAVGAQGEVNYA 300

Query: 303 LEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYAR 362
           LEG+VFM GA+IQWLRDE+ LI DA D+EYFA+KV +TNGVY+VPAF GLGAPYWDP AR
Sbjct: 301 LEGSVFMGGATIQWLRDELGLIRDASDTEYFASKVADTNGVYLVPAFVGLGAPYWDPNAR 360

Query: 363 GAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQF 422
           GA+FGLTRG N NHIIRA LESIAYQ++D+L+AM  DSG+ L  L+VDGGAVAN+FLMQF
Sbjct: 361 GALFGLTRGANRNHIIRAALESIAYQSKDLLDAMIKDSGVSLKRLKVDGGAVANDFLMQF 420

Query: 423 QSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNY 482
           Q+DI    V RP V E TALGAA+LAGLAVGFW ++ EL+ KA I+  F+P I    R  
Sbjct: 421 QADITDVEVLRPSVCETTALGAAFLAGLAVGFWNSVTELEHKACIDTHFKPSINADYRQQ 480

Query: 483 RYAGWKKAVKR 493
            YAGW+ AV R
Sbjct: 481 LYAGWQDAVAR 491


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: 813
Number of extensions: 18
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: 502
Length of database: 494
Length adjustment: 34
Effective length of query: 468
Effective length of database: 460
Effective search space:   215280
Effective search space used:   215280
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 203312 SO4230 (glycerol kinase (NCBI ptt file))
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.24171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-227  741.8   0.1   1.5e-227  741.7   0.1    1.0  1  lcl|FitnessBrowser__MR1:203312  SO4230 glycerol kinase (NCBI ptt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203312  SO4230 glycerol kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  741.7   0.1  1.5e-227  1.5e-227       1     494 [.       4     493 ..       4     494 .] 0.99

  Alignments for each domain:
  == domain 1  score: 741.7 bits;  conditional E-value: 1.5e-227
                       TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGitnq 79 
                                     k+++a+DqGttssraivfd+++++v+ +q+e++q +p++gwvEhdp+ei++s+ +vl e+l++++i+++ +aaiGitnq
  lcl|FitnessBrowser__MR1:203312   4 KYVVALDQGTTSSRAIVFDHDANIVSVSQREFTQLYPNPGWVEHDPMEIWASQSSVLIESLARAGIHSDAVAAIGITNQ 82 
                                     69***************************************************************************** PP

                       TIGR01311  80 REttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaeegell 158
                                     REtt++W+k+tgkp++naivWq++r a+i+e+lk+++ e+++r++tGL+l++Yfs+tK++W+ldnv+++r++a++gell
  lcl|FitnessBrowser__MR1:203312  83 RETTIIWEKATGKPVYNAIVWQCRRSAEICEQLKAQGLEDYVRQNTGLLLDPYFSGTKIKWILDNVPDARAKAKRGELL 161
                                     ******************************************************************************* PP

                       TIGR01311 159 fGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekellkeevpit 237
                                     fGtvdtwl++kLt+gkvhvtd tNA+Rtll+n+++l+wd++lle+++ip+++lPe+++s +vyg+++ +   ++e+p++
  lcl|FitnessBrowser__MR1:203312 162 FGTVDTWLLWKLTEGKVHVTDPTNAARTLLFNIHSLSWDSKLLEALDIPAAMLPEVKPSCSVYGTTRIA-GEGSEIPLA 239
                                     *****************************************************************9998.89******* PP

                       TIGR01311 238 gvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlr 316
                                     g++Gdqqaal+gqlc+++g+aKntYgtGcFll+ntG+k+v s+hglLttva   +g+   +yalEGsv+++Ga++qwlr
  lcl|FitnessBrowser__MR1:203312 240 GIAGDQQAALFGQLCVEQGMAKNTYGTGCFLLMNTGSKAVRSSHGLLTTVAVGAQGEV--NYALEGSVFMGGATIQWLR 316
                                     ***************************************************9999877..6****************** PP

                       TIGR01311 317 dnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileame 395
                                     d+l+li++a+++e +a++v d++gvy+VPaf GL+aPyWd++Arg+++Gltr+++++hi+raale++a+q++d+l+am 
  lcl|FitnessBrowser__MR1:203312 317 DELGLIRDASDTEYFASKVADTNGVYLVPAFVGLGAPYWDPNARGALFGLTRGANRNHIIRAALESIAYQSKDLLDAMI 395
                                     ******************************************************************************* PP

                       TIGR01311 396 kdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepem 474
                                     kd+gv++k LkvDGg+++n++lmq+qadi +v+v rp+v ettalGaA++aglavg+w+s +ele++a  + ++f+p++
  lcl|FitnessBrowser__MR1:203312 396 KDSGVSLKRLKVDGGAVANDFLMQFQADITDVEVLRPSVCETTALGAAFLAGLAVGFWNSVTELEHKACID-THFKPSI 473
                                     ******************************************************************99997.9****** PP

                       TIGR01311 475 deeerekkykkwkeaversl 494
                                     +++ r++ y+ w++av+r++
  lcl|FitnessBrowser__MR1:203312 474 NADYRQQLYAGWQDAVARTR 493
                                     *****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (494 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: 00:00:00.02
# Mc/sec: 11.11
//
[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