Alignments for a candidate for glpK in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Shewanella amazonensis SB2B

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate 6936144 Sama_0341 glycerol kinase (RefSeq)

Query= CharProtDB::CH_121461
         (502 letters)



>FitnessBrowser__SB2B:6936144
          Length = 495

 Score =  718 bits (1853), Expect = 0.0
 Identities = 342/494 (69%), Positives = 415/494 (84%), Gaps = 1/494 (0%)

Query: 3   EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLV 62
           +K+Y+VALDQGTTSSRA+V D DAN+++VSQREF QIYPK GWVEHDPMEIWA+QSSTL+
Sbjct: 2   DKQYVVALDQGTTSSRAIVFDRDANLVAVSQREFTQIYPKGGWVEHDPMEIWASQSSTLI 61

Query: 63  EVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLE 122
           EVLA+A I SD++AAIGITNQRETTI+W+K TGKP+ NAIVWQCRR+A ICE LK  GLE
Sbjct: 62  EVLARAGIHSDEVAAIGITNQRETTIIWDKLTGKPVCNAIVWQCRRSAAICEALKAQGLE 121

Query: 123 DYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVT 182
              R  TGL++DPYFSGTK+KWILD+V G RERA  GELLFGTVDTWL+WK+T+G+VHVT
Sbjct: 122 PLFRDKTGLLLDPYFSGTKIKWILDNVPGVRERADAGELLFGTVDTWLVWKLTEGKVHVT 181

Query: 183 DYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISG 242
           D TNASRT+++NIH+ +WD ++L+ LDIP  +LPEV+ S  VYG T I G+G T IP++G
Sbjct: 182 DPTNASRTLMYNIHSGEWDSELLKALDIPASLLPEVKSSQAVYGTTRIAGEG-TEIPVAG 240

Query: 243 IAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYA 302
           +AGDQQAALFGQLCV+ GMAKNTYGTGCF+LMNTG++AVKSE+GLLTTIA G  G ++YA
Sbjct: 241 MAGDQQAALFGQLCVEPGMAKNTYGTGCFLLMNTGKQAVKSEHGLLTTIAVGDDGGISYA 300

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

Query: 363 GAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQF 422
           G + GLTRG N NHIIRA LESIAYQ+RD+L+AM  DSG+ L  L+VDGGAVAN+FLMQF
Sbjct: 361 GTLVGLTRGANRNHIIRAALESIAYQSRDLLDAMSKDSGVALKQLKVDGGAVANDFLMQF 420

Query: 423 QSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNY 482
           Q+DI G  V RP   E TA+GAA+L GLAVGFW N+DE++ K+ I+R F P ++  ER  
Sbjct: 421 QADISGVEVLRPAQTETTAMGAAFLGGLAVGFWSNVDEIRHKSGIDRRFVPLMDDKERAT 480

Query: 483 RYAGWKKAVKRAMA 496
            Y GW+ AV+R+++
Sbjct: 481 LYLGWQDAVRRSLS 494


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: 815
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: 495
Length adjustment: 34
Effective length of query: 468
Effective length of database: 461
Effective search space:   215748
Effective search space used:   215748
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 6936144 Sama_0341 (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.19240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.9e-226  737.0   0.0   4.4e-226  736.8   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6936144  Sama_0341 glycerol kinase (RefSe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936144  Sama_0341 glycerol kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.8   0.0  4.4e-226  4.4e-226       1     494 [.       4     493 ..       4     495 .] 0.99

  Alignments for each domain:
  == domain 1  score: 736.8 bits;  conditional E-value: 4.4e-226
                         TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGit 77 
                                       ++++a+DqGttssraivfd++++ va +q+e++qi+pk gwvEhdp+ei++s+ ++l e+l++++i+++e+aaiGit
  lcl|FitnessBrowser__SB2B:6936144   4 QYVVALDQGTTSSRAIVFDRDANLVAVSQREFTQIYPKGGWVEHDPMEIWASQSSTLIEVLARAGIHSDEVAAIGIT 80 
                                       69*************************************************************************** PP

                         TIGR01311  78 nqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaee 154
                                       nqREtt++Wdk tgkp++naivWq++r a i+e+lk+++ e  +r+ktGL+l++Yfs+tK++W+ldnv++vr++a++
  lcl|FitnessBrowser__SB2B:6936144  81 NQRETTIIWDKLTGKPVCNAIVWQCRRSAAICEALKAQGLEPLFRDKTGLLLDPYFSGTKIKWILDNVPGVRERADA 157
                                       ***************************************************************************** PP

                         TIGR01311 155 gellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekellk 231
                                       gellfGtvdtwl++kLt+gkvhvtd tNASRtl++n+++ +wd+ell++++ip++llPe++ss++vyg+++ +   +
  lcl|FitnessBrowser__SB2B:6936144 158 GELLFGTVDTWLVWKLTEGKVHVTDPTNASRTLMYNIHSGEWDSELLKALDIPASLLPEVKSSQAVYGTTRIA-GEG 233
                                       *********************************************************************9998.89* PP

                         TIGR01311 232 eevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvava 308
                                       +e+p++g++Gdqqaal+gqlc+++g+aKntYgtGcFll+ntG+++v s+hglLtt+a   +g    +yalEG+v+++
  lcl|FitnessBrowser__SB2B:6936144 234 TEIPVAGMAGDQQAALFGQLCVEPGMAKNTYGTGCFLLMNTGKQAVKSEHGLLTTIAVGDDGGI--SYALEGAVFMG 308
                                       *********************************************************9877766..6********** PP

                         TIGR01311 309 GaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavaf 385
                                       Ga++qwlrd+l+li++a+++e +a++v+d++gvy+VPaf GL+aPyWd+dArgt+vGltr+++++hi+raale++a+
  lcl|FitnessBrowser__SB2B:6936144 309 GATIQWLRDELGLIRDASDTEYFASKVDDTNGVYLVPAFVGLGAPYWDPDARGTLVGLTRGANRNHIIRAALESIAY 385
                                       ***************************************************************************** PP

                         TIGR01311 386 qardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleks 462
                                       q+rd+l+am+kd+gv +k+LkvDGg+++n++lmq+qadi gv+v rp ++etta+GaA++ glavg+w++ +e++++
  lcl|FitnessBrowser__SB2B:6936144 386 QSRDLLDAMSKDSGVALKQLKVDGGAVANDFLMQFQADISGVEVLRPAQTETTAMGAAFLGGLAVGFWSNVDEIRHK 462
                                       ***************************************************************************** PP

                         TIGR01311 463 aeaeektfepemdeeerekkykkwkeaversl 494
                                       +  + ++f p md++er++ y  w++av+rsl
  lcl|FitnessBrowser__SB2B:6936144 463 SGID-RRFVPLMDDKERATLYLGWQDAVRRSL 493
                                       **98.*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (495 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: 7.08
//
[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