GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Lentibacillus jeotgali Grbi

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_010532354.1 ON01_RS17690 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P39912
         (358 letters)



>NCBI__GCF_000224785.1:WP_010532354.1
          Length = 360

 Score =  548 bits (1413), Expect = e-161
 Identities = 272/350 (77%), Positives = 313/350 (89%), Gaps = 1/350 (0%)

Query: 1   MSNTELELLRQKADELNLQILKLINERGNVVKEIGKAKEAQGVNRFDPVRERTMLNNIIE 60
           MSN ELE LRQ+ D +N ++L LIN+R  +V++IG+ KE Q +NRFDPVRER MLN + +
Sbjct: 1   MSN-ELEQLRQQLDGVNNELLDLINQRAEIVQQIGQVKEKQSINRFDPVRERKMLNELTQ 59

Query: 61  NNDGPFENSTIQHIFKEIFKAGLELQEEDHSKALLVSRKKKPEDTIVDIKGEKIGDGQQR 120
            N+GPFENSTI+HIFKEIFKA LELQE+DH KALLVSRK+KPEDT++DIKGEK+GDG   
Sbjct: 60  KNNGPFENSTIEHIFKEIFKASLELQEDDHRKALLVSRKRKPEDTVIDIKGEKVGDGNLH 119

Query: 121 FIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGLGVEGLQILKRVADE 180
            I+GPC+VE+YEQV+EVA + K++G+K+LRGGAFKPRTSPYDFQGLGVEGLQILKRVADE
Sbjct: 120 HIMGPCSVENYEQVSEVAKSVKQKGLKMLRGGAFKPRTSPYDFQGLGVEGLQILKRVADE 179

Query: 181 FDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLLKRGLAATISE 240
            DLAV+SEIV PAH+E+ALDY+DVIQIGARNMQNFELLKAAG   KPVLLKRGL+ATISE
Sbjct: 180 QDLAVVSEIVNPAHVEKALDYVDVIQIGARNMQNFELLKAAGETNKPVLLKRGLSATISE 239

Query: 241 FINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPVFVDVTHSTGR 300
           F+NAAEYI S+GN  IILCERGIRTYE ATRNTLDISAVPILKQETHLPV VDVTHSTGR
Sbjct: 240 FVNAAEYINSRGNGDIILCERGIRTYEKATRNTLDISAVPILKQETHLPVMVDVTHSTGR 299

Query: 301 RDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKWLNEL 350
           RD+LLP AKAA+AIGADGVMAEVHPDP+VALSD+AQQM IP FE ++NEL
Sbjct: 300 RDILLPAAKAAVAIGADGVMAEVHPDPAVALSDAAQQMDIPTFENFMNEL 349


Lambda     K      H
   0.316    0.134    0.369 

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: 474
Number of extensions: 14
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: 358
Length of database: 360
Length adjustment: 29
Effective length of query: 329
Effective length of database: 331
Effective search space:   108899
Effective search space used:   108899
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_010532354.1 ON01_RS17690 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01801 (aroA: chorismate mutase (EC 5.4.99.5))

# 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/TIGR01801.hmm
# target sequence database:        /tmp/gapView.3419331.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01801  [M=102]
Accession:   TIGR01801
Description: CM_A: chorismate mutase
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-46  142.7   4.3    3.5e-46  141.9   4.3    1.4  1  NCBI__GCF_000224785.1:WP_010532354.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532354.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9   4.3   3.5e-46   3.5e-46       1     102 []       1     101 [.       1     101 [. 0.99

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 3.5e-46
                             TIGR01801   1 msnqeleslraevdelnrqilkliskrGevvkkiGkakeaqGvnrydParekemlneliesnkGPfedatikq 73 
                                           msn ele+lr+++d +n+++l+li++r e+v++iG+ ke+q  nr+dP+re++mlnel ++n+GPfe++ti++
  NCBI__GCF_000224785.1:WP_010532354.1   1 MSN-ELEQLRQQLDGVNNELLDLINQRAEIVQQIGQVKEKQSINRFDPVRERKMLNELTQKNNGPFENSTIEH 72 
                                           888.9******************************************************************** PP

                             TIGR01801  74 ifkeifkaslelqesedkkallvsrkvkp 102
                                           ifkeifkaslelqe++++kallvsrk kp
  NCBI__GCF_000224785.1:WP_010532354.1  73 IFKEIFKASLELQEDDHRKALLVSRKRKP 101
                                           ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (102 nodes)
Target sequences:                          1  (360 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: 24.35
//
[ok]

This GapMind analysis is from Jul 26 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