Alignments for a candidate for thrB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Sinorhizobium meliloti 1021

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate SMc00017 SMc00017 homoserine kinase

Query= reanno::Korea:Ga0059261_3253
         (319 letters)



>FitnessBrowser__Smeli:SMc00017
          Length = 326

 Score =  288 bits (737), Expect = 1e-82
 Identities = 146/310 (47%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYT ++ + L  FLA Y+VG L S KGIAEGVENSN+L+ TT+  +ILTLYEKRV A 
Sbjct: 1   MAVYTDITEDELIRFLAAYEVGSLTSYKGIAEGVENSNFLLHTTKGAYILTLYEKRVNAD 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           DLP+F+GL+ HLA +GL  P  +    G  +  L+GRPA +I FL G+ L  P     R 
Sbjct: 61  DLPFFLGLMHHLAERGLSCPLPLPRADGKLLGTLSGRPAAVISFLEGMWLRKPEAQHCRE 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
            G A+A MH+A   FPL RPN++ V+ W+PL+       D++  GL D++   +A +   
Sbjct: 121 VGRALASMHQAGEGFPLKRPNALSVEGWRPLWRNSEARADEVQAGLKDEIATELAFIEEH 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240
           W + D     IHADLFPDNV   GD+++GLIDFYFAC D   YD+A+  ++W F+  G +
Sbjct: 181 WPK-DLPEGVIHADLFPDNVFFLGDRLSGLIDFYFACNDFLAYDVAICLNSWCFEKDG-S 238

Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300
           Y+   G AL++GYE+   LT  E  A P LA G+ +RF L+R +DWL TP  ALV++KDP
Sbjct: 239 YNITKGMALLSGYESVRRLTAEEIEALPLLARGSALRFFLTRLYDWLMTPPGALVVKKDP 298

Query: 301 LAYVRRLKHY 310
           L Y+ +++ +
Sbjct: 299 LEYLTKIRFH 308


Lambda     K      H
   0.323    0.138    0.429 

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: 308
Number of extensions: 12
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: 319
Length of database: 326
Length adjustment: 28
Effective length of query: 291
Effective length of database: 298
Effective search space:    86718
Effective search space used:    86718
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate SMc00017 SMc00017 (homoserine kinase)
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.18559.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.9e-125  404.2   0.0   2.1e-125  404.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00017  SMc00017 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00017  SMc00017 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.0   0.0  2.1e-125  2.1e-125       1     306 [.       1     306 [.       1     307 [. 0.99

  Alignments for each domain:
  == domain 1  score: 404.0 bits;  conditional E-value: 2.1e-125
                           TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaer 75 
                                         mavyt+++++el  fL  y++G l s kGiaeGvensn+ll t+kg y+Ltlyekrv+a++LPffl l++hLaer
  lcl|FitnessBrowser__Smeli:SMc00017   1 MAVYTDITEDELIRFLAAYEVGSLTSYKGIAEGVENSNFLLHTTKGAYILTLYEKRVNADDLPFFLGLMHHLAER 75 
                                         9************************************************************************** PP

                           TIGR00938  76 glpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsi 150
                                         gl+++ p+++ dG++l++L+G+Paa+++fL+G+ ++kP a++crevg  la +h ag++f+ +r n l+ e W++
  lcl|FitnessBrowser__Smeli:SMc00017  76 GLSCPLPLPRADGKLLGTLSGRPAAVISFLEGMWLRKPEAQHCREVGRALASMHQAGEGFPLKRPNALSVEGWRP 150
                                         *************************************************************************** PP

                           TIGR00938 151 laakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklkgvidfyfaCedallydla 225
                                         l  +    +++++++l++++ +el+++++ +p+dLP+gvihadlf+dnv++ gd+l+g+idfyfaC+d l+yd+a
  lcl|FitnessBrowser__Smeli:SMc00017 151 LWRNSEARADEVQAGLKDEIATELAFIEEHWPKDLPEGVIHADLFPDNVFFLGDRLSGLIDFYFACNDFLAYDVA 225
                                         ***99999******************************************************************* PP

                           TIGR00938 226 iavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPae 300
                                         i++n Wcfe+d+++++++  all gye+vr L++ee +a+p l+rg+alrf+l+rl d+ +t++g+lvv kdP e
  lcl|FitnessBrowser__Smeli:SMc00017 226 ICLNSWCFEKDGSYNITKGMALLSGYESVRRLTAEEIEALPLLARGSALRFFLTRLYDWLMTPPGALVVKKDPLE 300
                                         *************************************************************************** PP

                           TIGR00938 301 ferkLk 306
                                         +  k++
  lcl|FitnessBrowser__Smeli:SMc00017 301 YLTKIR 306
                                         *98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (326 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: 10.77
//
[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