GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Salinicoccus carnicancri Crm

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_017550016.1 C792_RS0113615 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

Query= reanno::psRCH2:GFF155
         (247 letters)



>NCBI__GCF_000330705.1:WP_017550016.1
          Length = 233

 Score =  163 bits (412), Expect = 3e-45
 Identities = 94/228 (41%), Positives = 131/228 (57%), Gaps = 9/228 (3%)

Query: 1   MLIIPAIDLKDGACVRLRQGLMDDATVFSDDP---VAMAAKWVEAGCRRLHLVDLNGAFE 57
           M IIPAID+ DG  VRL+QG  D  T     P   +   + + + G  R+H+VDL GA +
Sbjct: 1   MNIIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGFRQVG--RIHIVDLMGALK 58

Query: 58  GQPVNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEA 117
                  V+  + K   DLP+QIGGG+R +ETI  Y R G+ Y I+GTKA+ +  ++ EA
Sbjct: 59  QDAQESTVIEKL-KSQTDLPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEA 117

Query: 118 CRAFPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQG 177
            R FPG++ VG DA++  +  +GW E S +   +  R  E   ++ I+YTDI KDGM QG
Sbjct: 118 VREFPGRIFVGTDARENDIYVNGWTENSDITIDEYIREIEGLDIAGIIYTDINKDGMNQG 177

Query: 178 CNVEATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRA 225
            N E T  +   +R  VIASGG+ N  D+ KL      G+  AI G+A
Sbjct: 178 PNFENTRRINELTRHKVIASGGVRNKEDLDKL---GALGVRDAIVGKA 222


Lambda     K      H
   0.320    0.138    0.405 

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: 170
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: 247
Length of database: 233
Length adjustment: 23
Effective length of query: 224
Effective length of database: 210
Effective search space:    47040
Effective search space used:    47040
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 WP_017550016.1 C792_RS0113615 (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.527561.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-73  232.3   0.7    3.3e-73  232.1   0.7    1.0  1  NCBI__GCF_000330705.1:WP_017550016.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017550016.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.1   0.7   3.3e-73   3.3e-73       1     227 [.       3     229 ..       3     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.1 bits;  conditional E-value: 3.3e-73
                             TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfee.egaellHvVDLdgAkegekknlevikkiveele 72 
                                           iiPaiD+++G+ vrl qGd+d++t ++++p+ea++ ++    + ++H+VDL gA ++ +++++vi+k++++++
  NCBI__GCF_000330705.1:WP_017550016.1   3 IIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGfRQVGRIHIVDLMGALKQDAQESTVIEKLKSQTD 75 
                                           8************************************997789****************************** PP

                             TIGR00007  73 vkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksel 145
                                           +++q+GGG+R++e+++++ ++g+++ i+gt+a+ +++++ke+++e+   +i+v+ Da+e+++ v+GW+e+s++
  NCBI__GCF_000330705.1:WP_017550016.1  76 LPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEAVREFP-GRIFVGTDARENDIYVNGWTENSDI 147
                                           **********************************************9.************************* PP

                             TIGR00007 146 slvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkklgvkgvivG 218
                                           ++ e ++++e l++++ii+Tdi+kdG+ +G+n+e t+++ + ++ +viasGGv+++ed+ +l +lgv+++ivG
  NCBI__GCF_000330705.1:WP_017550016.1 148 TIDEYIREIEGLDIAGIIYTDINKDGMNQGPNFENTRRINELTRHKVIASGGVRNKEDLDKLGALGVRDAIVG 220
                                           ************************************************************************* PP

                             TIGR00007 219 kAlyegklk 227
                                           kA ++ +++
  NCBI__GCF_000330705.1:WP_017550016.1 221 KASHNDSFW 229
                                           ***999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (233 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: 20.41
//
[ok]

This GapMind analysis is from Jul 26 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