GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom_kinase in Azospirillum brasilense Sp245

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate AZOBR_RS10500 AZOBR_RS10500 homoserine kinase

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



>FitnessBrowser__azobra:AZOBR_RS10500
          Length = 327

 Score =  278 bits (710), Expect = 2e-79
 Identities = 139/310 (44%), Positives = 197/310 (63%), Gaps = 2/310 (0%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYT+V+ + L  F+A+YD+G ++S KGIAEGVENSN+L+ T R  +ILTLYEKR    
Sbjct: 1   MAVYTEVTDDELNAFIAQYDLGAVLSCKGIAEGVENSNFLLVTERGPYILTLYEKRTRRE 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           DLP+F+GL++HLA KG+  P  ++   G+ ++EL GRPA ++ FL+G+     TP     
Sbjct: 61  DLPFFLGLMEHLADKGIACPLPVQGTDGLALRELAGRPAVIVTFLAGMWPRRITPHHCAE 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
            G A+A++H AVADF ++RPN++ +D W+ L  KC    D++   L   L   +A +   
Sbjct: 121 LGTALARLHLAVADFRMERPNALSLDGWKDLAGKCAPRADEVARDLRATLEAELAALEAN 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGRN 240
           W         IHADLFPDNV  RGD ++GLIDFYFAC D   YD+A+  +AW F+  G +
Sbjct: 181 WPAG-LPSGVIHADLFPDNVFFRGDGLSGLIDFYFACNDFLAYDIAICMNAWCFEVDG-S 238

Query: 241 YDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKDP 300
           ++      L+  Y+   PL+  E AA P L  G+ +RF L+R +DWLN P  A V  KDP
Sbjct: 239 FNATKARMLLTSYQKVRPLSPAEMAALPWLCRGSALRFLLTRLYDWLNHPPGAFVRPKDP 298

Query: 301 LAYVRRLKHY 310
           L Y+R+L+ +
Sbjct: 299 LEYLRKLRFH 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: 285
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: 327
Length adjustment: 28
Effective length of query: 291
Effective length of database: 299
Effective search space:    87009
Effective search space used:    87009
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 AZOBR_RS10500 AZOBR_RS10500 (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.16440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-125  403.6   0.0   3.3e-125  403.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS10500  AZOBR_RS10500 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS10500  AZOBR_RS10500 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.4   0.0  3.3e-125  3.3e-125       1     307 []       1     307 [.       1     307 [. 1.00

  Alignments for each domain:
  == domain 1  score: 403.4 bits;  conditional E-value: 3.3e-125
                                 TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 
                                               mavyt+v+d+el+af+  ydlG++ls kGiaeGvensn+ll t++g y+Ltlyekr++ e+LPffl l+
  lcl|FitnessBrowser__azobra:AZOBR_RS10500   1 MAVYTEVTDDELNAFIAQYDLGAVLSCKGIAEGVENSNFLLVTERGPYILTLYEKRTRREDLPFFLGLM 69 
                                               9******************************************************************** PP

                                 TIGR00938  70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138
                                               +hLa++g++++ pv+  dG al eLaG+Pa++v fL+G+  ++ t+++c+e g  la+lhla adf+ e
  lcl|FitnessBrowser__azobra:AZOBR_RS10500  70 EHLADKGIACPLPVQGTDGLALRELAGRPAVIVTFLAGMWPRRITPHHCAELGTALARLHLAVADFRME 138
                                               ********************************************************************* PP

                                 TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207
                                               r n l+l+ W+ la k+   ++++ ++l a+l++el+al+ ++p  LP+gvihadlf+dnv++ gd+l+
  lcl|FitnessBrowser__azobra:AZOBR_RS10500 139 RPNALSLDGWKDLAGKCAPRADEVARDLRATLEAELAALEANWPAGLPSGVIHADLFPDNVFFRGDGLS 207
                                               ********************************************************************* PP

                                 TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276
                                               g+idfyfaC+d l+yd+ai++n+Wcfe d++++a++a+ ll +y++vrpLs+ e aa+p l rg+alrf
  lcl|FitnessBrowser__azobra:AZOBR_RS10500 208 GLIDFYFACNDFLAYDIAICMNAWCFEVDGSFNATKARMLLTSYQKVRPLSPAEMAALPWLCRGSALRF 276
                                               ********************************************************************* PP

                                 TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLkv 307
                                               ll+rl d+ + ++g++v++kdP e+ rkL++
  lcl|FitnessBrowser__azobra:AZOBR_RS10500 277 LLTRLYDWLNHPPGAFVRPKDPLEYLRKLRF 307
                                               ****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (327 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: 00:00:00.00
# Mc/sec: 11.74
//
[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:

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