Alignments for a candidate for thrB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Caulobacter crescentus NA1000

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate CCNA_03475 CCNA_03475 homoserine kinase

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



>FitnessBrowser__Caulo:CCNA_03475
          Length = 317

 Score =  265 bits (678), Expect = 8e-76
 Identities = 142/316 (44%), Positives = 194/316 (61%), Gaps = 3/316 (0%)

Query: 1   MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETTRDRFILTLYEKRVEAA 60
           MAVYT ++ + L  FL  YD+G  ++ KGIAEGVENSN+L+ET + R+ILT+YE+RV+A 
Sbjct: 1   MAVYTDITDQELEAFLEGYDLGAPLAFKGIAEGVENSNFLLETEKGRYILTVYERRVKAE 60

Query: 61  DLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTPAQARA 120
           DLPYF+ +L  LA +G P    I  R G  +  L G+PA +++FL G+S+  PT A  R 
Sbjct: 61  DLPYFLNMLTWLADRGYPSARPIPTRSGATLSSLRGKPAAIVEFLPGLSVRKPTAAHCRE 120

Query: 121 AGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHSLDQIVPGLYDDLGFAIARVVPA 180
           AGE +A +H A   +P  R N +G   W PLF K   + + + PGL   +   +A++   
Sbjct: 121 AGEGLAWLHLAGEGYPGRRANDLGQAAWSPLFSKHRKAAEDLKPGLSATIDNDLAQLSLM 180

Query: 181 WTRNDFDRCAIHADLFPDNVLMRGD-QVTGLIDFYFACTDIRVYDLAVMHSAWSFDAHGR 239
           W RN      IHAD FPDNV  + + +    IDFYFAC D   YD+AV  +AW F+A G 
Sbjct: 181 WPRN-LPTGTIHADYFPDNVFFQSNGKFAAAIDFYFACDDAYAYDVAVTLNAWCFEADG- 238

Query: 240 NYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADALVMRKD 299
           +++     AL+ GYE   PL+ +E+ A P LA GA +RF L+R  DW +TPA ALV  KD
Sbjct: 239 SFNITAAKALLNGYERRRPLSPIEKEALPILARGAAMRFFLTRLADWGSTPAGALVRPKD 298

Query: 300 PLAYVRRLKHYAPDLV 315
           PL Y R+L  +   LV
Sbjct: 299 PLEYERKLAVHREGLV 314


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: 286
Number of extensions: 10
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: 319
Length of database: 317
Length adjustment: 27
Effective length of query: 292
Effective length of database: 290
Effective search space:    84680
Effective search space used:    84680
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 CCNA_03475 CCNA_03475 (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.2018376.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-156  506.0   0.0   2.2e-156  505.8   0.0    1.0  1  FitnessBrowser__Caulo:CCNA_03475  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_03475  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.8   0.0  2.2e-156  2.2e-156       1     306 [.       1     307 [.       1     308 [. 0.99

  Alignments for each domain:
  == domain 1  score: 505.8 bits;  conditional E-value: 2.2e-156
                         TIGR00938   1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflellthLaergl 77 
                                       mavyt+++d+eleafLegydlG++l++kGiaeGvensn+ll+t+kgry+Lt+ye+rvkae+LP+fl++lt+La+rg+
  FitnessBrowser__Caulo:CCNA_03475   1 MAVYTDITDQELEAFLEGYDLGAPLAFKGIAEGVENSNFLLETEKGRYILTVYERRVKAEDLPYFLNMLTWLADRGY 77 
                                       9**************************************************************************** PP

                         TIGR00938  78 pvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkeerkndlrleaWsilaak 154
                                       p+a+p+++r+G++ls+L+GkPaa+vefL+G+sv+kPta++cre+ge la+lhlag++++++r+ndl+++aWs+l++k
  FitnessBrowser__Caulo:CCNA_03475  78 PSARPIPTRSGATLSSLRGKPAAIVEFLPGLSVRKPTAAHCREAGEGLAWLHLAGEGYPGRRANDLGQAAWSPLFSK 154
                                       ***************************************************************************** PP

                         TIGR00938 155 kfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdk.lkgvidfyfaCedallydlaiavnd 230
                                       ++k++e+l+++l+a++d++l++l+ ++pr+LP+g+ihad+f+dnv++++++ ++++idfyfaC+da++yd+a+++n+
  FitnessBrowser__Caulo:CCNA_03475 155 HRKAAEDLKPGLSATIDNDLAQLSLMWPRNLPTGTIHADYFPDNVFFQSNGkFAAAIDFYFACDDAYAYDVAVTLNA 231
                                       *************************************************988************************* PP

                         TIGR00938 231 WcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306
                                       Wcfead++++++aakall+gye++rpLs++ek+a+p+l+rgaa+rf+l+rl+d+ +t+ag+lv++kdP e+erkL+
  FitnessBrowser__Caulo:CCNA_03475 232 WCFEADGSFNITAAKALLNGYERRRPLSPIEKEALPILARGAAMRFFLTRLADWGSTPAGALVRPKDPLEYERKLA 307
                                       **************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (317 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: 17.98
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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