GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Azospirillum brasilense Sp245

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate AZOBR_RS01680 AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= reanno::azobra:AZOBR_RS01680
         (249 letters)



>FitnessBrowser__azobra:AZOBR_RS01680
          Length = 249

 Score =  490 bits (1262), Expect = e-143
 Identities = 249/249 (100%), Positives = 249/249 (100%)

Query: 1   MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60
           MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP
Sbjct: 1   MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60

Query: 61  VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120
           VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF
Sbjct: 61  VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120

Query: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180
           PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE
Sbjct: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180

Query: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLLS 240
           ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLLS
Sbjct: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLLS 240

Query: 241 PAPVTGKAG 249
           PAPVTGKAG
Sbjct: 241 PAPVTGKAG 249


Lambda     K      H
   0.318    0.138    0.401 

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: 419
Number of extensions: 21
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: 249
Length of database: 249
Length adjustment: 24
Effective length of query: 225
Effective length of database: 225
Effective search space:    50625
Effective search space used:    50625
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: 46 (22.3 bits)

Align candidate AZOBR_RS01680 AZOBR_RS01680 (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.3589.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.1e-87  278.6   0.1    2.4e-87  278.4   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS01680  AZOBR_RS01680 1-(5-phosphoribosy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS01680  AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.4   0.1   2.4e-87   2.4e-87       1     230 [.       3     234 ..       3     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.4 bits;  conditional E-value: 2.4e-87
                                 TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 
                                               i+PaiDlk+G++vrl++G++++ tv++++p+++a+ fe++g+e+lH+VDL+gA+eg+++n +++++i+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS01680   3 IYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKPVNGKAVESILG 71 
                                               89******************************************************************* PP

                                 TIGR00007  70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138
                                               +++++vq+GGGiR+l++++++le+gv+rvi+gt+a+++pelv+e+ +e+   k++v++Da+eg vav G
  lcl|FitnessBrowser__azobra:AZOBR_RS01680  72 AVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREFP-GKVAVGIDAREGYVAVAG 139
                                               *************************************************9.9***************** PP

                                 TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207
                                               W+e+s++++++la k+e+ g+++ii+Tdi++dG + Gvnve+t++l+ + +++viasGGvssi+d++al
  lcl|FitnessBrowser__azobra:AZOBR_RS01680 140 WAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVEATSDLAFHLTTPVIASGGVSSIDDLIAL 208
                                               ********************************************************************* PP

                                 TIGR00007 208 kk...lgvkgvivGkAlyegklklke 230
                                               kk   +g++gvi+G+Aly+g+++ k+
  lcl|FitnessBrowser__azobra:AZOBR_RS01680 209 KKeedTGIEGVICGRALYDGRIDPKT 234
                                               *99999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (249 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 5.85
//
[ok]

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

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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