GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB 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.3505976.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 19.16
//
[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:

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