Alignments for a candidate for hom_kinase in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Acidovorax sp. GW101-3H11

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate Ac3H11_1651 Homoserine kinase (EC 2.7.1.39)

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1651
          Length = 316

 Score =  209 bits (531), Expect = 9e-59
 Identities = 127/318 (39%), Positives = 170/318 (53%), Gaps = 10/318 (3%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           M+VFT +  +     L    LG L + RGI  G EN+N+F++ + G FVLTL ER   + 
Sbjct: 1   MAVFTEVSNTEARELLRRLQLGELVELRGIEGGIENTNYFLTSDQGAFVLTLFERLTAEQ 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           LPF++ L+  L   G+PVP     ++G+ L  + GKPA +  +L G+ +  P   HC  V
Sbjct: 61  LPFYLYLMKHLAHGGVPVPDPRADKNGDILHTVCGKPAAVVNKLRGKSQLAPQGAHCAAV 120

Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALA--EIAALDA 178
           G +L  +H A R     +P+ RGLPW  E    + P + E   ALL   LA     A  +
Sbjct: 121 GTMLARMHLAGRDFDRRQPNLRGLPWWNETVPVVLPHIGEAQSALLRAELAYQNHVAAGS 180

Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSN-TDGSL 237
              ALP   +HADLFRDNV+F+G  L G  DFY A     L+DLA+ LNDWC +   G+ 
Sbjct: 181 AYAALPCGPVHADLFRDNVMFEGEELTGFFDFYFAGVDTWLFDLAVCLNDWCIDLPTGAH 240

Query: 238 DPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRL----IAAEAFAGQDVLIH 293
           D  RA  +L AY   RP TA E E  P+MLR   +RFW+SRL    +  EA     +  H
Sbjct: 241 DAERATRMLDAYQAVRPLTAAERELLPAMLRAGALRFWISRLWDFYLPREA---SMLTPH 297

Query: 294 DPAEFEIRLAQRQNVEIH 311
           DP  FE  L  R    +H
Sbjct: 298 DPTHFERVLRHRVAHPVH 315


Lambda     K      H
   0.324    0.140    0.434 

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: 272
Number of extensions: 12
Number of successful extensions: 4
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: 316
Length of database: 316
Length adjustment: 27
Effective length of query: 289
Effective length of database: 289
Effective search space:    83521
Effective search space used:    83521
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate Ac3H11_1651 (Homoserine kinase (EC 2.7.1.39))
to HMM TIGR00938 (thrB: homoserine kinase (EC 2.7.1.39))

# 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.aa/TIGR00938.hmm
# target sequence database:        /tmp/gapView.6525.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00938  [M=307]
Accession:   TIGR00938
Description: thrB_alt: homoserine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.8e-100  321.1   0.0   4.3e-100  320.9   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651  Homoserine kinase (EC 2.7.1.39)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651  Homoserine kinase (EC 2.7.1.39)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.9   0.0  4.3e-100  4.3e-100       1     307 []       1     308 [.       1     308 [. 0.97

  Alignments for each domain:
  == domain 1  score: 320.9 bits;  conditional E-value: 4.3e-100
                                        TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeL 62 
                                                      mav+t+vs+ e ++ L    lGel++l+Gi  G+en+ny+lt d+g +vLtl+e+ + ae+L
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651   1 MAVFTEVSNTEARELLRRLQLGELVELRGIEGGIENTNYFLTSDQGAFVLTLFERLT-AEQL 61 
                                                      9*******************************************************9.**** PP

                                        TIGR00938  63 PfflellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgev 124
                                                      Pf+l l++hLa+ g+pv+ p + ++G  l ++ GkPaa+v+ L+G+s   P+ ++c++vg +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651  62 PFYLYLMKHLAHGGVPVPDPRADKNGDILHTVCGKPAAVVNKLRGKSQLAPQGAHCAAVGTM 123
                                                      ************************************************************** PP

                                        TIGR00938 125 laklhlagadfkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp.... 182
                                                      la++hlag df+ ++ n lr   W+ ++     vl+++ e ++all++el++ +++ +    
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 124 LARMHLAGRDFDRRQPN-LRGLPWWNETVPV--VLPHIGEAQSALLRAELAYQNHVAAgsay 182
                                                      *****************.***********99..*******************9998752333 PP

                                        TIGR00938 183 rdLPrgvihadlfkdnvlldgdklkgvidfyfaCedallydlaiavndWcfea.ddkldaaa 243
                                                        LP g +hadlf+dnv+++g++l+g+ dfyfa  d++l+dla+++ndWc++   +  da++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 183 AALPCGPVHADLFRDNVMFEGEELTGFFDFYFAGVDTWLFDLAVCLNDWCIDLpTGAHDAER 244
                                                      68**************************************************72568899** PP

                                        TIGR00938 244 akallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkL 305
                                                      a  +l++y+avrpL++ e++ +p +lr++alrf++srl+d++ ++   + ++ dP++fer L
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 245 ATRMLDAYQAVRPLTAAERELLPAMLRAGALRFWISRLWDFYLPREASMLTPHDPTHFERVL 306
                                                      *************************************************************9 PP

                                        TIGR00938 306 kv 307
                                                      ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1651 307 RH 308
                                                      86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (316 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: 00:00:00.01
# Mc/sec: 8.51
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis