GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrB in Escherichia coli BW25113

Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate 14148 b0003 homoserine kinase (NCBI)

Query= CharProtDB::CH_002113
         (310 letters)



>FitnessBrowser__Keio:14148
          Length = 310

 Score =  626 bits (1614), Expect = 0.0
 Identities = 310/310 (100%), Positives = 310/310 (100%)

Query: 1   MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEP 60
           MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEP
Sbjct: 1   MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEP 60

Query: 61  RENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLND 120
           RENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLND
Sbjct: 61  RENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLND 120

Query: 121 TRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGI 180
           TRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGI
Sbjct: 121 TRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGI 180

Query: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP 240
           KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP
Sbjct: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP 240

Query: 241 GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRL 300
           GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRL
Sbjct: 241 GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRL 300

Query: 301 DTAGARVLEN 310
           DTAGARVLEN
Sbjct: 301 DTAGARVLEN 310


Lambda     K      H
   0.321    0.136    0.412 

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: 463
Number of extensions: 5
Number of successful extensions: 1
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: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 14148 b0003 (homoserine kinase (NCBI))
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.10064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.2e-126  406.8   0.0   2.5e-126  406.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:14148  b0003 homoserine kinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14148  b0003 homoserine kinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.6   0.0  2.5e-126  2.5e-126       1     303 [.       2     309 ..       2     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 406.6 bits;  conditional E-value: 2.5e-126
                       TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk.sleaegegvekipkesdkNliyqvakkvlkklgkrv 78 
                                     +kv++PassAN+++GfDvlG+a+++v+++l++++v++e++++ sl++ g++++k+p+e+++N++yq++++++++lgk+ 
  lcl|FitnessBrowser__Keio:14148   2 VKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETfSLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQ- 79 
                                     69****************************************9***********************************. PP

                       TIGR00191  79 kpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlavked 151
                                      pv++t+ek++p+g+GLGSSa+++vaa++a+ne++g++l++++ll+l+++lEg      H+DNvap++lGG+ql+++e+
  lcl|FitnessBrowser__Keio:14148  80 IPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGrisgsiHYDNVAPCFLGGMQLMIEEN 158
                                     ******************************************************************************* PP

                       TIGR00191 152 dllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvhqpyR 230
                                     d +++++vP ++++ +vl++P+i+vsTaeaRa+LP++y+rqd++++++hla++++A++s+ +++l+a++mkD++++pyR
  lcl|FitnessBrowser__Keio:14148 159 D-IISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSR-QPELAAKLMKDVIAEPYR 235
                                     *.**********************************************************.****************** PP

                       TIGR00191 231 ekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkvleldtdgaevek 303
                                     e+l+P++++ +qa++e ga+++++SG+Gpt++al+++ + +++++++l k++ +++e++v++++ldt+ga+v++
  lcl|FitnessBrowser__Keio:14148 236 ERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPEtAQRVADWLGKNYLQNQEGFVHICRLDTAGARVLE 309
                                     ***************************************9*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (310 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: 11.49
//
[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