GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Marinobacter adhaerens HP15

Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate GFF3067 HP15_3011 imidazole glycerol phosphate synthase subunit HisH

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



>FitnessBrowser__Marino:GFF3067
          Length = 225

 Score =  210 bits (534), Expect = 2e-59
 Identities = 107/211 (50%), Positives = 131/211 (62%), Gaps = 3/211 (1%)

Query: 1   MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60
           M  + ++DYGMGNL S  +A+ HVAP+  V ++     IR ADRV+LPG GA+ DCM  +
Sbjct: 13  MKTVAIIDYGMGNLHSAKKAVEHVAPDTTVLVTDNAEKIREADRVILPGVGAIRDCMAEM 72

Query: 61  RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDD 119
              GV D V E S+ +P  G+CVG Q L   SEE G    +GL P +V  F       ++
Sbjct: 73  HRLGVVDLVREVSQDRPFLGICVGMQALMSRSEENGGVDCIGLFPSQVRYFG--DHLTEN 130

Query: 120 GSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFAC 179
           G   KVP MGWN V QT  HPLW  I +   FYFVHS+YA    +A + G+T YG D A 
Sbjct: 131 GERLKVPHMGWNQVQQTIDHPLWHNIPEGDRFYFVHSFYAEAEGNADMAGRTRYGVDLAA 190

Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFVHW 210
           AVARDNIFA QFHPEKSA AGLQL  NF +W
Sbjct: 191 AVARDNIFAVQFHPEKSARAGLQLLENFTNW 221


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: 171
Number of extensions: 6
Number of successful extensions: 2
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: 225
Length adjustment: 22
Effective length of query: 190
Effective length of database: 203
Effective search space:    38570
Effective search space used:    38570
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 GFF3067 HP15_3011 (imidazole glycerol phosphate synthase subunit HisH)
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.7096.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    2.1e-68  216.1   0.0    2.5e-68  215.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3067  HP15_3011 imidazole glycerol pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3067  HP15_3011 imidazole glycerol phosphate synthase subunit HisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.0   2.5e-68   2.5e-68       1     197 [.      16     220 ..      16     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 2.5e-68
                           TIGR01855   1 ivvidygvgNlksvkkalervg..aesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvvkkkk 72 
                                         +++idyg+gNl+s kka+e+v   +++ v+++++++++ad+++lPGVGa +++m+++++l+ ++l+  ++v++++
  lcl|FitnessBrowser__Marino:GFF3067  16 VAIIDYGMGNLHSAKKAVEHVApdTTVLVTDNAEKIREADRVILPGVGAIRDCMAEMHRLGvVDLV--REVSQDR 88 
                                         79******************97214555677789***************************55555..6788899 PP

                           TIGR01855  73 pvlgiClGmQllfekseEgkevkglglikgkvkkleaek.......kvPhiGWnevevvkesellkgleeearvY 140
                                         p+lgiC+GmQ l+++seE++ v+++gl++ +v+ + ++        kvPh+GWn+v+ + +++l +++ e++r+Y
  lcl|FitnessBrowser__Marino:GFF3067  89 PFLGICVGMQALMSRSEENGGVDCIGLFPSQVRYFGDHLtengerlKVPHMGWNQVQQTIDHPLWHNIPEGDRFY 163
                                         ********************************98877666667899***************************** PP

                           TIGR01855 141 fvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                         fvHs+++e e + ++   + yg ++ aav++dni++vQFHPEkS+++Gl+ll+nf++
  lcl|FitnessBrowser__Marino:GFF3067 164 FVHSFYAEAEGNADMAGRTRYGVDLAAAVARDNIFAVQFHPEKSARAGLQLLENFTN 220
                                         *******************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (225 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: 5.39
//
[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