Alignments for a candidate for glpK in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Burkholderia phytofirmans PsJN

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate BPHYT_RS16495 BPHYT_RS16495 glycerol kinase

Query= CharProtDB::CH_121461
         (502 letters)



>FitnessBrowser__BFirm:BPHYT_RS16495
          Length = 499

 Score =  642 bits (1655), Expect = 0.0
 Identities = 302/497 (60%), Positives = 391/497 (78%), Gaps = 1/497 (0%)

Query: 3   EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLV 62
           + +YI+ALDQGTTSSRA++ D   NI+S +Q+EF+QIYP+PGWVEHDP EIW+TQ+    
Sbjct: 2   QDQYILALDQGTTSSRAMLFDRLGNIVSTAQKEFQQIYPRPGWVEHDPQEIWSTQAGVAA 61

Query: 63  EVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLE 122
           E + +A ++   IAAIGITNQRETTIVW++ETG PIYNAIVWQ RRTA+ C+ LK  GLE
Sbjct: 62  EAVTRAGMNGTSIAAIGITNQRETTIVWDRETGHPIYNAIVWQDRRTADFCDQLKEQGLE 121

Query: 123 DYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVT 182
           + +R+ TGL ID YFS TK++WILD+VEG+RE+AR+G L FGTVD+WL+W  T+G +HVT
Sbjct: 122 EKVRAKTGLPIDSYFSATKIRWILDNVEGAREKARQGRLAFGTVDSWLVWNFTKGGLHVT 181

Query: 183 DYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISG 242
           D TNASRTMLFNIH+L WDD++LE LDIPR MLPEVR SSEVYG T       ++IP++G
Sbjct: 182 DVTNASRTMLFNIHSLKWDDELLEALDIPRSMLPEVRASSEVYGPTKT-TVFASKIPLAG 240

Query: 243 IAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYA 302
           IAGDQ AALFGQ+C + GM KNTYGTGCF++MNTG+K ++S+N L+TTIA     ++NYA
Sbjct: 241 IAGDQHAALFGQMCTESGMVKNTYGTGCFLVMNTGDKPIESKNNLVTTIAWQIGDQINYA 300

Query: 303 LEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYAR 362
           LEG++F+ GA +QWLRD + +I +A + E  A  V +++GVY+VPAF GLGAP+W+  AR
Sbjct: 301 LEGSIFIGGAVVQWLRDGLGIIKNAAEIETLARSVSHSDGVYLVPAFAGLGAPHWNARAR 360

Query: 363 GAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQF 422
           G +FG+TRG ++ HI RA L+SIAYQ+ DVL+AM+ADSGIR+  LRVDGGA ANN LMQF
Sbjct: 361 GTLFGVTRGTSSAHIARAALDSIAYQSLDVLKAMEADSGIRIGELRVDGGACANNLLMQF 420

Query: 423 QSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNY 482
           Q+DILG    RP+V E TALGAAYLAGLAVG+W+++DELQ +  ++R F P +   E   
Sbjct: 421 QADILGVDAVRPKVAETTALGAAYLAGLAVGYWKDVDELQSQWKLDRRFTPALPHAEVKQ 480

Query: 483 RYAGWKKAVKRAMAWEE 499
              GW++A++ A AW +
Sbjct: 481 CLDGWQRAIRAAKAWAD 497


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: 787
Number of extensions: 19
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: 499
Length adjustment: 34
Effective length of query: 468
Effective length of database: 465
Effective search space:   217620
Effective search space used:   217620
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 BPHYT_RS16495 BPHYT_RS16495 (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.5437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.8e-230  750.7   1.6   3.2e-230  750.5   1.6    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16495  BPHYT_RS16495 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16495  BPHYT_RS16495 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  750.5   1.6  3.2e-230  3.2e-230       1     496 []       4     495 ..       4     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 750.5 bits;  conditional E-value: 3.2e-230
                                TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                              ++i+a+DqGttssra++fd+ g++v++aqke++qi+p++gwvEhdp+ei++++  v+aea+++++++ + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495   4 QYILALDQGTTSSRAMLFDRLGNIVSTAQKEFQQIYPRPGWVEHDPQEIWSTQAGVAAEAVTRAGMNGTS 73 
                                              69******************************************************************** PP

                                TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrW 140
                                              iaaiGitnqREtt+vWd+etg+p++naivWqd+rta+++++lke++ ee++r+ktGLp+++YfsatK+rW
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495  74 IAAIGITNQRETTIVWDRETGHPIYNAIVWQDRRTADFCDQLKEQGLEEKVRAKTGLPIDSYFSATKIRW 143
                                              ********************************************************************** PP

                                TIGR01311 141 lldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkel 210
                                              +ldnve++r++a++g+l fGtvd+wl++++t+g+ hvtdvtNASRt+l+n+++lkwd+elle+++ip+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 144 ILDNVEGAREKARQGRLAFGTVDSWLVWNFTKGGLHVTDVTNASRTMLFNIHSLKWDDELLEALDIPRSM 213
                                              ********************************************************************** PP

                                TIGR01311 211 lPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkvisk 280
                                              lPe+r ssevyg ++++ ++ +++p++g++Gdq+aal+gq+c+++g++KntYgtGcFl++ntG+k++ sk
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 214 LPEVRASSEVYGPTKTT-VFASKIPLAGIAGDQHAALFGQMCTESGMVKNTYGTGCFLVMNTGDKPIESK 282
                                              ***************99.9*************************************************** PP

                                TIGR01311 281 hglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGL 350
                                              ++l+tt+a+++g++   +yalEGs++++Ga+vqwlrd l++ik+a+e+e+la+sv++s+gvy+VPaf+GL
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 283 NNLVTTIAWQIGDQI--NYALEGSIFIGGAVVQWLRDGLGIIKNAAEIETLARSVSHSDGVYLVPAFAGL 350
                                              ************987..5**************************************************** PP

                                TIGR01311 351 faPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqi 420
                                              +aP+W+++Argt++G+tr+t ++hiaraal+++a+q+ d+l+ame+d+g+++ +L+vDGg+++nnllmq+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 351 GAPHWNARARGTLFGVTRGTSSAHIARAALDSIAYQSLDVLKAMEADSGIRIGELRVDGGACANNLLMQF 420
                                              ********************************************************************** PP

                                TIGR01311 421 qadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeav 490
                                              qadilgv+ +rpkvaettalGaA++aglavg+wk+ +el+++++ + ++f+p+  ++e ++ +  w++a+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 421 QADILGVDAVRPKVAETTALGAAYLAGLAVGYWKDVDELQSQWKLD-RRFTPALPHAEVKQCLDGWQRAI 489
                                              *********************************************8.*********************** PP

                                TIGR01311 491 erslkw 496
                                              + ++ w
  lcl|FitnessBrowser__BFirm:BPHYT_RS16495 490 RAAKAW 495
                                              *99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (499 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: 11.21
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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