GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Marinobacter adhaerens HP15

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= reanno::pseudo5_N2C3_1:AO356_09800
         (245 letters)



>FitnessBrowser__Marino:GFF3066
          Length = 245

 Score =  373 bits (958), Expect = e-108
 Identities = 187/245 (76%), Positives = 204/245 (83%)

Query: 1   MLIIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQP 60
           MLIIPAIDLKDG CVRLRQGRM+DSTVF DDPV MA +WVE G RRLHLVDLNGAF G+P
Sbjct: 1   MLIIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEP 60

Query: 61  VNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRA 120
           VNGE+V AIA++YP+LPIQIGGGIRS ETIE Y+KAGV +VIIGTKAVKEPEFV E C+ 
Sbjct: 61  VNGEIVQAIARKYPDLPIQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKK 120

Query: 121 FPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCNV 180
           FPG +IVGLDAKDG VATDGWAEVS V   DLAKRF  DGV AIVYTDI++DGMMQG NV
Sbjct: 121 FPGHIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDGVDAIVYTDISRDGMMQGVNV 180

Query: 181 PFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYEGTLDVAEAQAFC 240
             TAALA    IPVIASGG+ N+ D+K L      GI+GAITGRAIYEGTLDVAEAQAFC
Sbjct: 181 EATAALAEEGGIPVIASGGVTNMDDLKRLATVADKGILGAITGRAIYEGTLDVAEAQAFC 240

Query: 241 DSYKG 245
           D  KG
Sbjct: 241 DGLKG 245


Lambda     K      H
   0.320    0.138    0.407 

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: 311
Number of extensions: 6
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: 245
Length of database: 245
Length adjustment: 24
Effective length of query: 221
Effective length of database: 221
Effective search space:    48841
Effective search space used:    48841
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: 46 (22.3 bits)

Align candidate GFF3066 HP15_3010 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

# 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/TIGR00007.hmm
# target sequence database:        /tmp/gapView.14780.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00007  [M=231]
Accession:   TIGR00007
Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    4.3e-85  271.0   2.1    4.9e-85  270.8   2.1    1.0  1  lcl|FitnessBrowser__Marino:GFF3066  HP15_3010 1-(5-phosphoribosyl)-5


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3066  HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imida
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.8   2.1   4.9e-85   4.9e-85       1     230 [.       3     235 ..       3     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 270.8 bits;  conditional E-value: 4.9e-85
                           TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveel.evk 74 
                                         iiPaiDlk+Gk+vrl qG++d +tv++ddp+++a+++ e ga++lH+VDL+gA++ge++n e+++ i+++  +++
  lcl|FitnessBrowser__Marino:GFF3066   3 IIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEPVNGEIVQAIARKYpDLP 77 
                                         8******************************************************************9886489* PP

                           TIGR00007  75 vqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslve 149
                                         +q+GGGiRs+e++e++l++gv+ viigt+av++pe+v+e+ k++   +i+v+lDak+g+va+ GW+e se+ +++
  lcl|FitnessBrowser__Marino:GFF3066  78 IQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKFP-GHIIVGLDAKDGRVATDGWAEVSEVMATD 151
                                         ********************************************9.99*************************** PP

                           TIGR00007 150 lakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk...lgvkgvivGkAl 221
                                         lak++++ g+++i++Tdi++dG+++Gvnve+t  l++e  ++viasGGv++++d+k+l++    g+ g+i G+A+
  lcl|FitnessBrowser__Marino:GFF3066 152 LAKRFANDGVDAIVYTDISRDGMMQGVNVEATAALAEEGGIPVIASGGVTNMDDLKRLATvadKGILGAITGRAI 226
                                         **********************************************************9877789999******* PP

                           TIGR00007 222 yegklklke 230
                                         yeg+l++ e
  lcl|FitnessBrowser__Marino:GFF3066 227 YEGTLDVAE 235
                                         *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (245 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: 7.89
//
[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