GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Paraburkholderia bryophila 376MFSha3.1

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate H281DRAFT_05658 H281DRAFT_05658 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= reanno::BFirm:BPHYT_RS17685
         (250 letters)



>FitnessBrowser__Burk376:H281DRAFT_05658
          Length = 250

 Score =  493 bits (1268), Expect = e-144
 Identities = 246/250 (98%), Positives = 249/250 (99%)

Query: 1   MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60
           MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWV+RGARRLHLVDLNGAFAGKP
Sbjct: 1   MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVERGARRLHLVDLNGAFAGKP 60

Query: 61  KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120
           +NE+AIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGL YVIIGTAAVKNPGFLQDACT
Sbjct: 61  RNEEAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLQDACT 120

Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180
           AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN
Sbjct: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180

Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240
           IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL
Sbjct: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240

Query: 241 ADRLRESDDA 250
           ADRLRESDDA
Sbjct: 241 ADRLRESDDA 250


Lambda     K      H
   0.319    0.140    0.410 

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: 391
Number of extensions: 3
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: 250
Length of database: 250
Length adjustment: 24
Effective length of query: 226
Effective length of database: 226
Effective search space:    51076
Effective search space used:    51076
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 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate H281DRAFT_05658 H281DRAFT_05658 ( 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.9175.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-82  261.8   0.2    3.2e-82  261.6   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05658  H281DRAFT_05658  1-(5-phosphorib


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05658  H281DRAFT_05658  1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.6   0.2   3.2e-82   3.2e-82       1     229 [.       3     235 ..       3     237 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.6 bits;  conditional E-value: 3.2e-82
                                    TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikk 66 
                                                  +iPaiDlk+G++vrl qGd+d+ t++s++p+++a+++ e ga++lH+VDL+gA++g+++n+e+i+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05658   3 LIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVERGARRLHLVDLNGAFAGKPRNEEAIRA 68 
                                                  59**************************************************************** PP

                                    TIGR00007  67 iveel..evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDak 130
                                                  i+ee+  e++vq+GGGiR+l+++e++l+ g+e+viigtaav+np +++++ +++g  +i+v+lDak
  lcl|FitnessBrowser__Burk376:H281DRAFT_05658  69 IIEEVggEIPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLQDACTAFG-GHIIVGLDAK 133
                                                  ***99445789********************************************.99******** PP

                                    TIGR00007 131 egevavkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasG 196
                                                  +g+va+ GW + +  ++++la+k+e++g+e+ii+Tdi +dG+l+G+n+e+t +l+++++++viasG
  lcl|FitnessBrowser__Burk376:H281DRAFT_05658 134 DGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGINIEATVRLARAVKIPVIASG 199
                                                  ****************************************************************** PP

                                    TIGR00007 197 Gvssiedvkalkk...lgvkgvivGkAlyegklklk 229
                                                  G s+ +d+++l +    g++gvi+G+A+y+g+l++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05658 200 GLSNLTDIESLCEvedEGIEGVICGRAIYSGDLDFA 235
                                                  *********998877799**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (250 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.38
//
[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