GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Azorhizobium caulinodans ORS 571

Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_012173019.1 AZC_RS23070 imidazole glycerol phosphate synthase subunit HisH

Query= BRENDA::Q5NMD4
         (213 letters)



>NCBI__GCF_000010525.1:WP_012173019.1
          Length = 215

 Score =  236 bits (601), Expect = 3e-67
 Identities = 121/215 (56%), Positives = 150/215 (69%), Gaps = 10/215 (4%)

Query: 8   TVALIDYGAGNLRSVANALLASGL--ARENLVVTANPDEVLQADRVVLPGVGAFASCMQA 65
           TVA++DYG+GNL S A A+  + L    E +VVT++PD V  ADRVVLPGVGAFA C + 
Sbjct: 2   TVAIVDYGSGNLHSAAKAIERAALDTGGERIVVTSDPDVVRAADRVVLPGVGAFADCRRG 61

Query: 66  LKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDP 125
           L A+P MV ALE+AV  +GRPFLGICVG+QLLA++G E+GV  GLGWIKG+V  + P+DP
Sbjct: 62  LDAVPGMVAALEEAVHGRGRPFLGICVGLQLLAERGLEHGVTAGLGWIKGEVDRITPSDP 121

Query: 126 SCKVPHMGWNQIGLTTDSHPLLR-------AGEAYFLHSYAFVPEDESTLLATTEHGGLV 178
             K+PHMGWN +     +H LL           AYF+HSYAF   D + LLATT++ G +
Sbjct: 122 DLKIPHMGWNTL-QPARAHALLEGIPLGPDGLHAYFVHSYAFKLADPADLLATTDYAGTI 180

Query: 179 TAAVGRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213
           TAAV RDN+ G QFHPEKSQ  GL  L+ FL W P
Sbjct: 181 TAAVARDNVAGTQFHPEKSQKLGLALLANFLKWRP 215


Lambda     K      H
   0.318    0.136    0.409 

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: 205
Number of extensions: 8
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: 213
Length of database: 215
Length adjustment: 22
Effective length of query: 191
Effective length of database: 193
Effective search space:    36863
Effective search space used:    36863
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate WP_012173019.1 AZC_RS23070 (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.967036.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-65  206.5   0.0      2e-65  206.4   0.0    1.0  1  NCBI__GCF_000010525.1:WP_012173019.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012173019.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.4   0.0     2e-65     2e-65       1     197 [.       3     212 ..       3     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 206.4 bits;  conditional E-value: 2e-65
                             TIGR01855   1 ivvidygvgNlksvkkalerv.....gaesevvkdskelekadklvlPGVGafkeamkklrele..lellaek 66 
                                           ++++dyg+gNl+s +ka+er+     g + +v++d + ++ ad++vlPGVGaf+++ + l      + +l+e 
  NCBI__GCF_000010525.1:WP_012173019.1   3 VAIVDYGSGNLHSAAKAIERAaldtgGERIVVTSDPDVVRAADRVVLPGVGAFADCRRGLDAVPgmVAALEEA 75 
                                           79***********99988876333336677899999*************************997777888889 PP

                             TIGR01855  67 vvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgle.. 134
                                           v  +++p+lgiC+G+Qll+e++ E++ + glg+ikg+v++++ +    k+Ph+GWn+++++++++ll+g+   
  NCBI__GCF_000010525.1:WP_012173019.1  76 VHGRGRPFLGICVGLQLLAERGLEHGVTAGLGWIKGEVDRITPSDpdlKIPHMGWNTLQPARAHALLEGIPlg 148
                                           9999**************************************988899**********************733 PP

                             TIGR01855 135 .eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197
                                            ++ ++YfvHsYa +l++  ++la++dy  +++aav++dn++g+QFHPEkS+k Gl+ll nfl+
  NCBI__GCF_000010525.1:WP_012173019.1 149 pDGLHAYFVHSYAFKLADPADLLATTDYAGTITAAVARDNVAGTQFHPEKSQKLGLALLANFLK 212
                                           356789********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (215 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.92
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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