GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Pseudomonas fluorescens FW300-N1B4

Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Pf1N1B4_1626 Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-)

Query= reanno::HerbieS:HSERO_RS20325
         (212 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626
          Length = 212

 Score =  198 bits (503), Expect = 7e-56
 Identities = 107/211 (50%), Positives = 127/211 (60%), Gaps = 4/211 (1%)

Query: 1   MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60
           M  + V+DYGMGNL SVA+AL HV     V I+ +   IR ADRVV PG GA+ DCM  +
Sbjct: 1   MQTVAVIDYGMGNLHSVAKALEHVGA-GKVLITSDADVIREADRVVFPGVGAIRDCMAEI 59

Query: 61  RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGD-TPGLGLLPGKVVRFDLEGMRQDD 119
           R  G    V E S+ +P  G+CVG Q L D SEE +    +GL PG+V  F  +    +D
Sbjct: 60  RRLGFDSLVREVSQDRPFLGICVGMQALLDSSEENNGVDCIGLFPGQVKFFGKD--LHED 117

Query: 120 GSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFAC 179
           G   KVP MGWN V QT  HPLW  I D A FYFVHSYY     +  VVG   YG DFA 
Sbjct: 118 GEHLKVPHMGWNEVKQTVEHPLWHNIPDLARFYFVHSYYIAAGNARQVVGSGHYGVDFAA 177

Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFVHW 210
           A+A  + FA QFHPEKS + GLQL +NF  W
Sbjct: 178 ALADGSRFAVQFHPEKSHTHGLQLLQNFAAW 208


Lambda     K      H
   0.322    0.137    0.431 

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: 165
Number of extensions: 6
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: 212
Length of database: 212
Length adjustment: 21
Effective length of query: 191
Effective length of database: 191
Effective search space:    36481
Effective search space used:    36481
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 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate Pf1N1B4_1626 (Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-))
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))

# 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/TIGR01855.hmm
# target sequence database:        /tmp/gapView.1205.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01855  [M=198]
Accession:   TIGR01855
Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    1.6e-68  216.5   0.0    1.8e-68  216.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626  Imidazole glycerol phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626  Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.3   0.0   1.8e-68   1.8e-68       1     197 [.       4     207 ..       4     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 216.3 bits;  conditional E-value: 1.8e-68
                                      TIGR01855   1 ivvidygvgNlksvkkalervgaese.vvkdskelekadklvlPGVGafkeamkklrelelell 63 
                                                    ++vidyg+gNl+sv+kale+vga ++ +++d++ +++ad++v+PGVGa +++m+++r+l+ + l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626   4 VAVIDYGMGNLHSVAKALEHVGAGKVlITSDADVIREADRVVFPGVGAIRDCMAEIRRLGFDSL 67 
                                                    79********************9655278899****************************8888 PP

                                      TIGR01855  64 aekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWne 120
                                                      ++v++++p+lgiC+GmQ l+++seE++ v+++gl++g+vk + ++        kvPh+GWne
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626  68 -VREVSQDRPFLGICVGMQALLDSSEENNGVDCIGLFPGQVKFFGKDLhedgehlKVPHMGWNE 130
                                                    .56677888********************************99988777788999********* PP

                                      TIGR01855 121 vevvkesellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkS 184
                                                    v+ + e++l +++ + ar+YfvHsY++   +  +v+ + +yg +f aa++++  ++vQFHPEkS
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626 131 VKQTVEHPLWHNIPDLARFYFVHSYYIAAGNARQVVGSGHYGVDFAAALADGSRFAVQFHPEKS 194
                                                    **************************************************************** PP

                                      TIGR01855 185 gktGlkllknfle 197
                                                    ++ Gl+ll+nf++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1626 195 HTHGLQLLQNFAA 207
                                                    ***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (212 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: 7.27
//
[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