Alignments for a candidate for glpK in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Sinorhizobium meliloti 1021

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate SM_b21009 SM_b21009 glycerol kinase

Query= reanno::Smeli:SM_b21009
         (497 letters)



>FitnessBrowser__Smeli:SM_b21009
          Length = 497

 Score = 1010 bits (2612), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60
           MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK
Sbjct: 1   MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60

Query: 61  EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120
           EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE
Sbjct: 61  EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120

Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180
           KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT
Sbjct: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180

Query: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240
           DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV
Sbjct: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240

Query: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300
           AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL
Sbjct: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300

Query: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360
           EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG
Sbjct: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360

Query: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420
           AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ
Sbjct: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420

Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480
           RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK
Sbjct: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480

Query: 481 VKLKGWRSAVKRTLIAA 497
           VKLKGWRSAVKRTLIAA
Sbjct: 481 VKLKGWRSAVKRTLIAA 497


Lambda     K      H
   0.319    0.134    0.415 

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: 1117
Number of extensions: 39
Number of successful extensions: 1
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate SM_b21009 SM_b21009 (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.15980.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   7.9e-221  719.5   0.1   9.8e-221  719.2   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21009  SM_b21009 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21009  SM_b21009 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  719.2   0.1  9.8e-221  9.8e-221       2     493 ..       4     493 ..       3     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 719.2 bits;  conditional E-value: 9.8e-221
                            TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiG 75 
                                          +i+aiDqGtts+raivfd ++++ +  qke++q+fpk+gwvEhdp+ei+++vv++++ea+ek++i+a++iaaiG
  lcl|FitnessBrowser__Smeli:SM_b21009   4 YILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVKEAIEKSGITANDIAAIG 77 
                                          9************************************************************************* PP

                            TIGR01311  76 itnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevr 149
                                          itnqREt+vvWd+etgkp++naivWqd+rta ++++lk+++ e+++ +ktGL+l++Yfs+tKl+Wll nv++++
  lcl|FitnessBrowser__Smeli:SM_b21009  78 ITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLEKTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQ 151
                                          ************************************************************************** PP

                            TIGR01311 150 kaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevyge 223
                                           +a +gel+fGt+dt+li++Ltgg+ ++td+tNASRtll+n+ +++wd+el e++++pke+lPe++++++ +g 
  lcl|FitnessBrowser__Smeli:SM_b21009 152 VRAAKGELCFGTIDTFLIWRLTGGECFCTDATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGV 225
                                          ************************************************************************** PP

                            TIGR01311 224 ieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkpt 297
                                          ++++ l+++++pi gv+Gdqqaa +gq+c+k+g+ K+tYgtGcF llntG+++v sk++lLtt+ay+l+g+++ 
  lcl|FitnessBrowser__Smeli:SM_b21009 226 TDPS-LFGAAIPILGVAGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETT- 297
                                          ****.*****************************************************************996. PP

                            TIGR01311 298 kyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrktt 371
                                           yalEGs++vaGaavqwlrd lk+ik a ++++la+s++ s++vy+VPaf+GL+aP+Wd+dArg+i+G+tr+t 
  lcl|FitnessBrowser__Smeli:SM_b21009 298 -YALEGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARGAIFGMTRNTG 370
                                          .************************************************************************* PP

                            TIGR01311 372 kehiaraaleavafqardileamekdagvevk..vLkvDGglsknnllmqiqadilgvkverpkvaettalGaA 443
                                           +++araaleav++q+rd+leam+kd   + +  vL+vDGg++++++ mq  +d+l+ +v rp + ettalG+A
  lcl|FitnessBrowser__Smeli:SM_b21009 371 PAEFARAALEAVCYQTRDLLEAMHKDWRRNGNdtVLRVDGGMVASDWTMQRLSDLLDAPVDRPVILETTALGVA 444
                                          **************************99665444**************************************** PP

                            TIGR01311 444 laaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeavers 493
                                          ++ag  +gvw ++e ++ks++++ ++fep+mde++r+ k+k w++av+r+
  lcl|FitnessBrowser__Smeli:SM_b21009 445 WLAGSRAGVWPNQEAFAKSWARD-RRFEPHMDEATRKVKLKGWRSAVKRT 493
                                          *********************98.************************98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.56
//
[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