Alignments for a candidate for glpK in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Phyllobacterium brassicacearum STM 196

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_106712325.1 CU102_RS17135 glycerol kinase GlpK

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



>NCBI__GCF_003010955.1:WP_106712325.1
          Length = 496

 Score =  793 bits (2048), Expect = 0.0
 Identities = 375/494 (75%), Positives = 430/494 (87%)

Query: 1   MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60
           M GY+LAIDQGTTS+RAI+FD N+K+ G  Q+EF Q +P+SGWVEHDPEEIWQ+V+ST +
Sbjct: 1   MNGYVLAIDQGTTSSRAIIFDKNRKVVGKSQQEFTQIYPQSGWVEHDPEEIWQSVLSTCQ 60

Query: 61  EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120
            AIE + I A D+AAIGITNQRETV+VWD+ TGKP+HNAIVWQDRRTA  C +LKK+GLE
Sbjct: 61  VAIENAKIHAGDVAAIGITNQRETVIVWDKATGKPVHNAIVWQDRRTAPICQRLKKQGLE 120

Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180
           KTF KKTGLLLDPYFSGTKL W+L  V GA+ RAA GEL FGT+D FLIWRLTGG+   T
Sbjct: 121 KTFTKKTGLLLDPYFSGTKLAWILDKVPGARKRAANGELLFGTVDCFLIWRLTGGKVHAT 180

Query: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240
           DATNASRTLL+NIA N WDDEL ++LR+P+ MLPEVKDCAA++G  +  LFGA IPILGV
Sbjct: 181 DATNASRTLLFNIATNEWDDELLDILRIPRAMLPEVKDCAANYGAAEAELFGATIPILGV 240

Query: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300
           AGDQ AATIGQACF+PGM KSTYGTGCFALLNTG DMV SKNRLLTTIAYRL+G+TTYAL
Sbjct: 241 AGDQHAATIGQACFEPGMFKSTYGTGCFALLNTGSDMVLSKNRLLTTIAYRLNGKTTYAL 300

Query: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360
           EGSIF+AGAAVQWLRDGLK+I +AP+TG LA+ ADPSQ VYLVPAF GLGAPHWD +ARG
Sbjct: 301 EGSIFIAGAAVQWLRDGLKIIGSAPETGKLADQADPSQNVYLVPAFVGLGAPHWDAEARG 360

Query: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420
           AI+G+TRNTGPAEFARAALE+V YQTRDLL+AM KDW+ +G  TVLRVDGGMVASDWTMQ
Sbjct: 361 AIYGLTRNTGPAEFARAALESVAYQTRDLLDAMRKDWKSSGTKTVLRVDGGMVASDWTMQ 420

Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480
           RL+D+LDAPVDRP ILETTALG AWLAGS+AG+WPN+  F+K+W RD +F P MDE TRK
Sbjct: 421 RLADILDAPVDRPEILETTALGAAWLAGSKAGIWPNRREFSKTWERDVQFTPKMDEKTRK 480

Query: 481 VKLKGWRSAVKRTL 494
            KL GW++AVKRTL
Sbjct: 481 TKLAGWKTAVKRTL 494


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: 924
Number of extensions: 37
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: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_106712325.1 CU102_RS17135 (glycerol kinase GlpK)
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.2103817.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-223  725.8   0.7   1.1e-222  725.7   0.7    1.0  1  NCBI__GCF_003010955.1:WP_106712325.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712325.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.7   0.7  1.1e-222  1.1e-222       2     494 ..       4     494 ..       3     496 .] 0.99

  Alignments for each domain:
  == domain 1  score: 725.7 bits;  conditional E-value: 1.1e-222
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           +++aiDqGttssrai+fdk+ ++v+k+q+e++qi+p++gwvEhdp+ei++sv+++++ a+e+++i+a ++aai
  NCBI__GCF_003010955.1:WP_106712325.1   4 YVLAIDQGTTSSRAIIFDKNRKVVGKSQQEFTQIYPQSGWVEHDPEEIWQSVLSTCQVAIENAKIHAGDVAAI 76 
                                           9************************************************************************ PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           GitnqREt++vWdk+tgkp++naivWqd+rta i+++lk+++ e+++++ktGL+l++Yfs+tKl+W+ld+v++
  NCBI__GCF_003010955.1:WP_106712325.1  77 GITNQRETVIVWDKATGKPVHNAIVWQDRRTAPICQRLKKQGLEKTFTKKTGLLLDPYFSGTKLAWILDKVPG 149
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                           +rk+a +gellfGtvd++li++Ltggkvh+td+tNASRtll+n+ t++wd+ell++++ip+++lPe++++++ 
  NCBI__GCF_003010955.1:WP_106712325.1 150 ARKRAANGELLFGTVDCFLIWRLTGGKVHATDATNASRTLLFNIATNEWDDELLDILRIPRAMLPEVKDCAAN 222
                                           ************************************************************************* PP

                             TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293
                                           yg  e++ l+++++pi gv+Gdq+aa +gq+c+++g+ K+tYgtGcF llntG+++v+sk++lLtt+ay+l+g
  NCBI__GCF_003010955.1:WP_106712325.1 223 YGAAEAE-LFGATIPILGVAGDQHAATIGQACFEPGMFKSTYGTGCFALLNTGSDMVLSKNRLLTTIAYRLNG 294
                                           ****999.***************************************************************** PP

                             TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366
                                           k++  yalEGs+++aGaavqwlrd lk+i +a e++kla +++ s++vy+VPaf GL+aP+Wd++Arg+i Gl
  NCBI__GCF_003010955.1:WP_106712325.1 295 KTT--YALEGSIFIAGAAVQWLRDGLKIIGSAPETGKLADQADPSQNVYLVPAFVGLGAPHWDAEARGAIYGL 365
                                           996..******************************************************************** PP

                             TIGR01311 367 trkttkehiaraaleavafqardileamekdagvevk..vLkvDGglsknnllmqiqadilgvkverpkvaet 437
                                           tr+t  +++araale+va+q+rd+l+am+kd +++ +  vL+vDGg++++++ mq  adil+ +v rp++ et
  NCBI__GCF_003010955.1:WP_106712325.1 366 TRNTGPAEFARAALESVAYQTRDLLDAMRKDWKSSGTktVLRVDGGMVASDWTMQRLADILDAPVDRPEILET 438
                                           *******************************997665459********************************* PP

                             TIGR01311 438 talGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                           talGaA++ag ++g+w + +e++k++e++  +f+p+mde++r++k++ wk+av+r+l
  NCBI__GCF_003010955.1:WP_106712325.1 439 TALGAAWLAGSKAGIWPNRREFSKTWERD-VQFTPKMDEKTRKTKLAGWKTAVKRTL 494
                                           ***************************98.9************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (496 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 24.30
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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