Alignments for a candidate for hom_kinase in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Dechlorosoma suillum PS

Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate Dsui_0456 Dsui_0456 homoserine kinase, Neisseria type

Query= SwissProt::P29364
         (316 letters)



>FitnessBrowser__PS:Dsui_0456
          Length = 313

 Score =  238 bits (608), Expect = 1e-67
 Identities = 142/311 (45%), Positives = 181/311 (58%), Gaps = 9/311 (2%)

Query: 1   MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60
           MSVFTP+ R  L+ +L+  D+G L DF GIA G +N+N+FV+   G +VLTL E     +
Sbjct: 1   MSVFTPVTREQLKDWLSGCDVGALADFAGIAAGVQNTNYFVTTGRGTWVLTLFETLGAAE 60

Query: 61  LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120
           L F++ L+  L   GLP P  +    G  LR L GKPA+L  RL G+    P   HC  V
Sbjct: 61  LDFYLGLMAHLARQGLPCPAPVADGAGAILRPLAGKPAVLVSRLTGQEVEAPGPAHCAAV 120

Query: 121 GDLLGHLH--AATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDA 178
           GD L  LH  AAT   + + P  RG  W  +  A + P L     ALL   LA  A    
Sbjct: 121 GDALARLHLAAATYDGVQDNP--RGEAWRRQAAAQVLPLLSGDDGALLQDELAYQAG--- 175

Query: 179 ERPALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLD 238
              ALP   +HADLFRDNVLF G  L+GL+DFY A    +L+DLA+  NDWC +  G+L+
Sbjct: 176 PAEALPEGLVHADLFRDNVLFQGERLSGLLDFYFAARDQLLFDLAVAANDWCLDGAGNLE 235

Query: 239 PARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEA-FAGQDVLIHDPAE 297
           P R RALL AY  RRP  A EA  WP +LR A +RFWLSRL    A  AG+ VL+ DP  
Sbjct: 236 PGRTRALLQAYHRRRPLQAAEARAWPRLLRRAALRFWLSRLQDFHAPRAGRQVLVKDPRH 295

Query: 298 F-EIRLAQRQN 307
           F ++ LA+R++
Sbjct: 296 FRDLLLARRRH 306


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: 309
Number of extensions: 18
Number of successful extensions: 3
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: 313
Length adjustment: 27
Effective length of query: 289
Effective length of database: 286
Effective search space:    82654
Effective search space used:    82654
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 Dsui_0456 Dsui_0456 (homoserine kinase, Neisseria type)
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.28403.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.7e-108  346.2   0.0     1e-107  346.0   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0456  Dsui_0456 homoserine kinase, Nei


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0456  Dsui_0456 homoserine kinase, Neisseria type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.0   0.0    1e-107    1e-107       1     305 [.       1     300 [.       1     302 [. 0.98

  Alignments for each domain:
  == domain 1  score: 346.0 bits;  conditional E-value: 1e-107
                         TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaergl 77 
                                       m+v+t v+ e+l+ +L+g d+G+l ++ Gia Gv+n+ny++tt +g +vLtl+e    a eL f+l l+ hLa +gl
  lcl|FitnessBrowser__PS:Dsui_0456   1 MSVFTPVTREQLKDWLSGCDVGALADFAGIAAGVQNTNYFVTTGRGTWVLTLFETLG-AAELDFYLGLMAHLARQGL 76 
                                       9*******************************************************9.99***************** PP

                         TIGR00938  78 pvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsilaak 154
                                       p+++pv+  +G+ l  LaGkPa+lv+ L+G++v+ P +++c++vg+ la+lhla+a +++ ++n +r eaW+ +aa+
  lcl|FitnessBrowser__PS:Dsui_0456  77 PCPAPVADGAGAILRPLAGKPAVLVSRLTGQEVEAPGPAHCAAVGDALARLHLAAATYDGVQDN-PRGEAWRRQAAA 152
                                       ****************************************************************.************ PP

                         TIGR00938 155 kfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklkgvidfyfaCedallydlaiavndW 231
                                       +  vl+ l+ +++all++el++     ++ LP+g++hadlf+dnvl++g++l+g++dfyfa +d+ll+dla+a ndW
  lcl|FitnessBrowser__PS:Dsui_0456 153 Q--VLPLLSGDDGALLQDELAYQA-GPAEALPEGLVHADLFRDNVLFQGERLSGLLDFYFAARDQLLFDLAVAANDW 226
                                       9..*****************9976.56789*********************************************** PP

                         TIGR00938 232 cfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkL 305
                                       c++  ++l+  +++all++y+++rpL + e  a+p llr aalrf+lsrl+d++ ++ag  v +kdP++f+ +L
  lcl|FitnessBrowser__PS:Dsui_0456 227 CLDGAGNLEPGRTRALLQAYHRRRPLQAAEARAWPRLLRRAALRFWLSRLQDFHAPRAGRQVLVKDPRHFRDLL 300
                                       **********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (313 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: 6.76
//
[ok]

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

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 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