Alignments for a candidate for hom_kinase in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom_kinase in Chlorobium phaeobacteroides BS1

Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate 642682810 Cphamn1_0296 homoserine kinase (EC 2.7.1.39)

Query= reanno::Cola:Echvi_2001
         (311 letters)



>IMG__ChlphaBS1_FD:642682810
          Length = 320

 Score =  298 bits (763), Expect = 1e-85
 Identities = 161/320 (50%), Positives = 209/320 (65%), Gaps = 12/320 (3%)

Query: 1   MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPG----VRVVRIEGDGGRLP 56
           MK VT FA AT+ NV+CGFD+LGFA+ E GD+V ++L +E      V +  I GDGG LP
Sbjct: 1   MKTVTGFASATIGNVACGFDVLGFAITEPGDEVILTLREERSGELPVSITSITGDGGALP 60

Query: 57  YEVDKNTCGVALKAFLA------AIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAAN 110
               KNT    +  FL        ID++G +E+EL K LPL SGMGSSAAS+ AAL AAN
Sbjct: 61  RNPKKNTSSFVVLKFLEYIRTNKGIDFEGHIELELKKNLPLSSGMGSSAASAAAALVAAN 120

Query: 111 QLLGNPLDKKALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGL 170
           +L+G P +K  L+ FA++ E VACG+ HADN AP++LG FVLIRSY+P+D+  +  P  L
Sbjct: 121 ELMGRPCNKMELVNFAIEGERVACGSAHADNAAPAMLGNFVLIRSYNPIDLITIPSPDNL 180

Query: 171 YCALVHPHLELNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIA 230
           YC LVHPH+E+ TA +RSVL + + LK A  Q GN+  L++GL   D  LI RSL DVIA
Sbjct: 181 YCTLVHPHIEVRTAYARSVLPRMISLKTATEQWGNVGALISGLLTSDYELIGRSLVDVIA 240

Query: 231 EPSRSVLIPGFDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFD--K 288
           EP R+ LIPGF ++K A  E GA+G  I+GSGP+ F  + S E A R  E  Q  F   K
Sbjct: 241 EPKRAPLIPGFYDVKHAALEAGAIGCSIAGSGPSIFAFSSSPETASRVGEAMQTAFSTLK 300

Query: 289 IGLEVDLYVSAVNTKGTYVI 308
             L+ D+++S V  +G  VI
Sbjct: 301 EKLQSDIWISPVCKQGAKVI 320


Lambda     K      H
   0.317    0.136    0.383 

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: 248
Number of extensions: 11
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: 311
Length of database: 320
Length adjustment: 27
Effective length of query: 284
Effective length of database: 293
Effective search space:    83212
Effective search space used:    83212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 642682810 Cphamn1_0296 (homoserine kinase (EC 2.7.1.39))
to HMM TIGR00191 (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/TIGR00191.hmm
# target sequence database:        /tmp/gapView.274217.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                    -----------
    8.9e-64  201.2   0.0      1e-63  201.0   0.0    1.0  1  IMG__ChlphaBS1_FD:642682810  


Domain annotation for each sequence (and alignments):
>> IMG__ChlphaBS1_FD:642682810  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.0     1e-63     1e-63       7     284 ..      10     299 ..       5     320 .] 0.86

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 1e-63
                    TIGR00191   7 assANlgpGfDvlGlalslvlellvtedvaqeskdk...sleaegegvekipkesdkNliyqvakkvlkklgkr.....vkp 80 
                                  a+  N++ GfDvlG a+++  + ++    +  s  +   s+++ + +   +p +++kN    v++k+l+    +        
  IMG__ChlphaBS1_FD:642682810  10 ATIGNVACGFDVLGFAITEPGDEVILTLREERSG-ElpvSITSITGDGGALPRNPKKNTSSFVVLKFLEYIRTNkgidfEGH 90 
                                  7889*************99865555553333333.2468999999999**********777666666654433323335567 PP

                    TIGR00191  81 vkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlavkeddllev 156
                                  ++l+++k++pl++G+GSSaa+ +aa++aanel+g +++k+el+++a++ E+      H+DN+apa+lG ++l  +++  +  
  IMG__ChlphaBS1_FD:642682810  91 IELELKKNLPLSSGMGSSAASAAAALVAANELMGRPCNKMELVNFAIEGERvacgsaHADNAAPAMLGNFVLIRSYNP-IDL 171
                                  99****************************************************************************.999 PP

                    TIGR00191 157 lkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelt 238
                                  + +Ps ++l++ lv P+iev Ta aR vLP+  s++ +  +  +++ l+  l +    +l+   + D++++p+R+ liP++ 
  IMG__ChlphaBS1_FD:642682810 172 ITIPSPDNLYCTLVHPHIEVRTAYARSVLPRMISLKTATEQWGNVGALISGLLTS-DYELIGRSLVDVIAEPKRAPLIPGFY 252
                                  999999*************************************************.6677777788**************** PP

                    TIGR00191 239 eikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakeg 284
                                  ++k+aa e+ga+g  + G+Gp+i+a+++  + + ++ e++++     
  IMG__ChlphaBS1_FD:642682810 253 DVKHAALEAGAIGCSIAGSGPSIFAFSSSPEtASRVGEAMQTAFSTL 299
                                  ***************************99998888888777655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (320 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: 15.72
//
[ok]

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