GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Synechococcus elongatus PCC 7942

Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Synpcc7942_1481 Synpcc7942_1481 imidazole glycerol phosphate synthase subunit HisH

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



>FitnessBrowser__SynE:Synpcc7942_1481
          Length = 217

 Score =  161 bits (408), Expect = 7e-45
 Identities = 92/209 (44%), Positives = 128/209 (61%), Gaps = 12/209 (5%)

Query: 3   KIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRE 62
           +I VVDY MGNL S  + L   A  A+  ++ + A I AAD V+LPG GA    M  LR+
Sbjct: 6   QIAVVDYDMGNLHSACKGLE--AAGANPIVTADPATILAADGVLLPGVGAFDPAMDHLRD 63

Query: 63  SGVQDAVIEASRT-KPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGS 121
             + + + +A+ + KP  G+C+G Q+LF+ SEEG + GLG+LPG+V RF     R + G 
Sbjct: 64  RQLIEPLHQAATSGKPFLGICLGLQLLFEASEEGQSAGLGILPGRVQRF-----RSEPGL 118

Query: 122 LFKVPQMGWNHVH-QTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYG-RDFAC 179
           +  +P MGWN +  Q    PLW+ +  + +FYFVH+YY VP+E         +G +    
Sbjct: 119 V--IPHMGWNQLQLQQPDCPLWQNLGADPWFYFVHTYYVVPSEPTLTAATVQHGSQPVTA 176

Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFV 208
           A+ARD ++A QFHPEKSA AGLQL  NFV
Sbjct: 177 AIARDRLWAVQFHPEKSAKAGLQLLANFV 205


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: 158
Number of extensions: 11
Number of successful extensions: 5
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: 217
Length adjustment: 22
Effective length of query: 190
Effective length of database: 195
Effective search space:    37050
Effective search space used:    37050
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 Synpcc7942_1481 Synpcc7942_1481 (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.13731.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.9e-66  209.7   0.0    2.1e-66  209.5   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1481  Synpcc7942_1481 imidazole glycer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1481  Synpcc7942_1481 imidazole glycerol phosphate synthase subunit HisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.5   0.0   2.1e-66   2.1e-66       1     196 [.       7     205 ..       7     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.5 bits;  conditional E-value: 2.1e-66
                                 TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 
                                               i+v+dy++gNl+s  k le++ga++ v++d  ++  ad ++lPGVGaf+ am++lr+++ +e l ++++
  lcl|FitnessBrowser__SynE:Synpcc7942_1481   7 IAVVDYDMGNLHSACKGLEAAGANPIVTADPATILAADGVLLPGVGAFDPAMDHLRDRQlIEPL-HQAA 74 
                                               79*********************************************************55555.9999 PP

                                 TIGR01855  69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvk.esellkgle 134
                                               +++kp+lgiClG+Qllfe seEg ++ glg+++g+v+++++e    +Ph+GWn+++ ++ +++l ++l 
  lcl|FitnessBrowser__SynE:Synpcc7942_1481  75 TSGKPFLGICLGLQLLFEASEEG-QSAGLGILPGRVQRFRSEPglVIPHMGWNQLQLQQpDCPLWQNLG 142
                                               9*********************6.68***************99999*********9987356******* PP

                                 TIGR01855 135 eearvYfvHsYaveleeeeavlakadyg.ekfvaavekdnivgvQFHPEkSgktGlkllknfl 196
                                               ++  +YfvH+Y+v+++e   + a++++g +  +aa+++d++ +vQFHPEkS+k+Gl+ll nf+
  lcl|FitnessBrowser__SynE:Synpcc7942_1481 143 ADPWFYFVHTYYVVPSEPTLTAATVQHGsQPVTAAIARDRLWAVQFHPEKSAKAGLQLLANFV 205
                                               ***************************626799****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (217 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: 6.37
//
[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