GapMind for Amino acid biosynthesis

 

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

Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate H281DRAFT_05657 H281DRAFT_05657 imidazole glycerol phosphate synthase subunit hisH

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



>FitnessBrowser__Burk376:H281DRAFT_05657
          Length = 213

 Score =  343 bits (879), Expect = 2e-99
 Identities = 164/209 (78%), Positives = 176/209 (84%)

Query: 4   IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63
           I +VDYGMGNLRSVAQALR  APEADV I  +   IRAADRVVLPGQGAMPDCMRSL ES
Sbjct: 5   IAIVDYGMGNLRSVAQALRKAAPEADVAIVDKPEAIRAADRVVLPGQGAMPDCMRSLAES 64

Query: 64  GVQDAVIEASRTKPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGSLF 123
           G+Q+AV+EASR KPL GVCVGEQMLFDWS EGDTPGLGLLPGKV+RFDLEG  QDDGS F
Sbjct: 65  GLQEAVVEASRVKPLMGVCVGEQMLFDWSAEGDTPGLGLLPGKVLRFDLEGQVQDDGSRF 124

Query: 124 KVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFACAVAR 183
           KVPQMGWN V Q   HPLW+G+ADNAFFYFVHSYY VP  +AH  G+T YG  F  AVAR
Sbjct: 125 KVPQMGWNRVRQALPHPLWDGVADNAFFYFVHSYYVVPENAAHTSGETVYGVPFTSAVAR 184

Query: 184 DNIFATQFHPEKSASAGLQLYRNFVHWKP 212
           DNIFATQFHPEKSA AGL++YRNFVHW P
Sbjct: 185 DNIFATQFHPEKSADAGLRVYRNFVHWNP 213


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: 249
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: 212
Length of database: 213
Length adjustment: 21
Effective length of query: 191
Effective length of database: 192
Effective search space:    36672
Effective search space used:    36672
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 H281DRAFT_05657 H281DRAFT_05657 (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.13659.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    3.4e-63  199.1   0.0    3.9e-63  198.9   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05657  H281DRAFT_05657 imidazole glycer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05657  H281DRAFT_05657 imidazole glycerol phosphate synthase subunit hisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.9   0.0   3.9e-63   3.9e-63       1     197 [.       5     210 ..       5     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 198.9 bits;  conditional E-value: 3.9e-63
                                    TIGR01855   1 ivvidygvgNlksvkkalerv..gaesevvkdskelekadklvlPGVGafkeamkklrelelella 64 
                                                  i+++dyg+gNl+sv++al+++  +a + +v++ ++++ ad++vlPG Ga+ ++m++l e++l+  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05657   5 IAIVDYGMGNLRSVAQALRKAapEADVAIVDKPEAIRAADRVVLPGQGAMPDCMRSLAESGLQEAV 70 
                                                  79****************9983356677888999***************************65553 PP

                                    TIGR01855  65 ekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.........kvPhiGWnev 121
                                                    ++++ kp++g+C+G Q+lf+ s Eg +++glgl++gkv +++ e          kvP++GWn+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05657  71 -VEASRVKPLMGVCVGEQMLFDWSAEG-DTPGLGLLPGKVLRFDLEGqvqddgsrfKVPQMGWNRV 134
                                                  .4555667******************7.68************98766667889999********** PP

                                    TIGR01855 122 evvkesellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgkt 187
                                                    +  ++l  g+ ++a +YfvHsY+v++e+  ++   + yg  f++av++dni+++QFHPEkS+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05657 135 RQALPHPLWDGVADNAFFYFVHSYYVVPENAAHTSGETVYGVPFTSAVARDNIFATQFHPEKSADA 200
                                                  ****************************************************************** PP

                                    TIGR01855 188 Glkllknfle 197
                                                  Gl++ +nf++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05657 201 GLRVYRNFVH 210
                                                  ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (213 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: 8.59
//
[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