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.8427.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.43
//
[ok]

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

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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:

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:

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:

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:

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