Alignments for a candidate for hisA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisA in Herbaspirillum seropedicae SmR1

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate HSERO_RS20320 HSERO_RS20320 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= reanno::HerbieS:HSERO_RS20320
         (265 letters)



>FitnessBrowser__HerbieS:HSERO_RS20320
          Length = 265

 Score =  527 bits (1358), Expect = e-155
 Identities = 265/265 (100%), Positives = 265/265 (100%)

Query: 1   MLLIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKP 60
           MLLIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKP
Sbjct: 1   MLLIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKP 60

Query: 61  KNEAAVKAILKAVASFAEENEVEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNP 120
           KNEAAVKAILKAVASFAEENEVEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNP
Sbjct: 61  KNEAAVKAILKAVASFAEENEVEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNP 120

Query: 121 GFLHDACSAFPGQIIVGLDAKDGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTDIGR 180
           GFLHDACSAFPGQIIVGLDAKDGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTDIGR
Sbjct: 121 GFLHDACSAFPGQIIVGLDAKDGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTDIGR 180

Query: 181 DGMMGGVNIEATVRLAQAVTIPIIASGGVHNVGDVEALCRVEDEGIEAVICGRSIYEGTL 240
           DGMMGGVNIEATVRLAQAVTIPIIASGGVHNVGDVEALCRVEDEGIEAVICGRSIYEGTL
Sbjct: 181 DGMMGGVNIEATVRLAQAVTIPIIASGGVHNVGDVEALCRVEDEGIEAVICGRSIYEGTL 240

Query: 241 DLRSGQDRADELTRELEANRLSGSK 265
           DLRSGQDRADELTRELEANRLSGSK
Sbjct: 241 DLRSGQDRADELTRELEANRLSGSK 265


Lambda     K      H
   0.318    0.138    0.400 

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: 439
Number of extensions: 9
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: 265
Length of database: 265
Length adjustment: 25
Effective length of query: 240
Effective length of database: 240
Effective search space:    57600
Effective search space used:    57600
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate HSERO_RS20320 HSERO_RS20320 (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.12063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.5e-76  242.4   0.4    3.5e-76  241.9   0.4    1.2  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20320  HSERO_RS20320 1-(5-phosphoribosy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20320  HSERO_RS20320 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylidenea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.9   0.4   3.5e-76   3.5e-76       1     229 [.       3     243 ..       3     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 241.9 bits;  conditional E-value: 3.5e-76
                                  TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiv 68 
                                                +iPaiDlk+G++vrl qGd+d+ tv+s+dp+e+a ++ ++ga++lH+VDL+gA++g++kn+ ++k i+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20320   3 LIPAIDLKDGHCVRLKQGDMDQATVFSEDPAEMALHWLKQGARRLHLVDLNGAFAGKPKNEAAVKAIL 70 
                                                59*****************************************************************9 PP

                                  TIGR00007  69 eel..........evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvs 126
                                                +++          e++vq+GGGiR+l+++e++l+ g++++iigtaav+np +++++ +++   +i+v+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20320  71 KAVasfaeeneveEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNPGFLHDACSAFP-GQIIVG 137
                                                8763333333333579********************************************9.99**** PP

                                  TIGR00007 127 lDakegevavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaevevia 194
                                                lDak+g+va+ GW + s  ++v+la+k+e +g+e+i++Tdi +dG++ Gvn+e+t +l++++++++ia
  lcl|FitnessBrowser__HerbieS:HSERO_RS20320 138 LDAKDGKVATDGWSKLSGHEVVDLAQKFEGYGCEAIVYTDIGRDGMMGGVNIEATVRLAQAVTIPIIA 205
                                                ******************************************************************** PP

                                  TIGR00007 195 sGGvssiedvkalkk...lgvkgvivGkAlyegklklk 229
                                                sGGv+++ dv+al +    g+++vi+G+ +yeg+l+l+
  lcl|FitnessBrowser__HerbieS:HSERO_RS20320 206 SGGVHNVGDVEALCRvedEGIEAVICGRSIYEGTLDLR 243
                                                ***********998766689999***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (265 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.78
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis