GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisC in Escherichia coli BW25113

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate 16129 b2021 histidinol-phosphate aminotransferase (NCBI)

Query= SwissProt::P06986
         (356 letters)



>lcl|FitnessBrowser__Keio:16129 b2021 histidinol-phosphate
           aminotransferase (NCBI)
          Length = 356

 Score =  707 bits (1825), Expect = 0.0
 Identities = 356/356 (100%), Positives = 356/356 (100%)

Query: 1   MSTVTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQP 60
           MSTVTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQP
Sbjct: 1   MSTVTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQP 60

Query: 61  KAVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETI 120
           KAVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETI
Sbjct: 61  KAVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETI 120

Query: 121 GVECRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAI 180
           GVECRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAI
Sbjct: 121 GVECRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAI 180

Query: 181 VVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVI 240
           VVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVI
Sbjct: 181 VVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVI 240

Query: 241 APYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYI 300
           APYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYI
Sbjct: 241 APYPLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYI 300

Query: 301 LARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV 356
           LARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV
Sbjct: 301 LARFKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV 356


Lambda     K      H
   0.319    0.135    0.396 

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: 604
Number of extensions: 13
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: 356
Length of database: 356
Length adjustment: 29
Effective length of query: 327
Effective length of database: 327
Effective search space:   106929
Effective search space used:   106929
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: 49 (23.5 bits)

Align candidate 16129 b2021 (histidinol-phosphate aminotransferase (NCBI))
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.31978.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.9e-131  423.0   0.0   4.4e-131  422.8   0.0    1.0  1  lcl|FitnessBrowser__Keio:16129  b2021 histidinol-phosphate amino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16129  b2021 histidinol-phosphate aminotransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.8   0.0  4.4e-131  4.4e-131       1     347 [.      11     352 ..      11     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 422.8 bits;  conditional E-value: 4.4e-131
                       TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenillgn 79 
                                     re++++l+pYq+ ar+lg++++v+Ln+nE+P++++     +l+++  +l+rYp++q++++ e++a+y+gv++e++l+++
  lcl|FitnessBrowser__Keio:16129  11 RENVRNLTPYQS-ARRLGGNGDVWLNANEYPTAVE----FQLTQQ--TLNRYPECQPKAVIENYAQYAGVKPEQVLVSR 82 
                                     799*********.9*******************99....899888..9******************************* PP

                       TIGR01141  80 Gsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPnnPtG 157
                                     G+de+ielliraf+epg da+l+++pty mY+vsa++ g+e+++vp+ +++q dl+ ++ ++ + vk+v+++sPnnPtG
  lcl|FitnessBrowser__Keio:16129  83 GADEGIELLIRAFCEPGkDAILYCPPTYGMYSVSAETIGVECRTVPTLDNWQLDLQGIS-DKLDGVKVVYVCSPNNPTG 160
                                     ***********************************************************.9****************** PP

                       TIGR01141 158 nllkreeiekvleeve.dalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekv 235
                                     +l++ ++++++le ++ +a+VV DeAYieF+++as + +laeyp+l++lrTlSKaf+LAglR+G+++an+e+i+ l+kv
  lcl|FitnessBrowser__Keio:16129 161 QLINPQDFRTLLELTRgKAIVVADEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKV 239
                                     ***************55************************************************************** PP

                       TIGR01141 236 rapynvsslaleaavaalrdsd..kiektveevkkererlleelkklegle.vyeSkaNFvlikvkedaeelleallek 311
                                     +apy++s++++++a +al+ +    ++++v+++++ere+l+++lk+++++e v++S++N++l+++k ++++++++l+++
  lcl|FitnessBrowser__Keio:16129 240 IAPYPLSTPVADIAAQALSPQGivAMRERVAQIIAEREYLIAALKEIPCVEqVFDSETNYILARFK-ASSAVFKSLWDQ 317
                                     **********************9999***************************************9.************ PP

                       TIGR01141 312 giivRdlksaeglleeclRitvGtreenerllealk 347
                                     gii+Rd++++++ l++clRitvGtree++r+++al+
  lcl|FitnessBrowser__Keio:16129 318 GIILRDQNKQPS-LSGCLRITVGTREESQRVIDALR 352
                                     ********9977.6********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.58
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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