GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase / chorismate mutase (EC 2.5.1.54; EC 5.4.99.5) (characterized)
to candidate Echvi_0120 Echvi_0120 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase

Query= reanno::Cola:Echvi_0120
         (367 letters)



>FitnessBrowser__Cola:Echvi_0120
          Length = 367

 Score =  750 bits (1936), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MKDHLKTSEWGLGLKGHVIIAGPCSAETPEQVEKVCLEMKEQNIIPSMFRAGIWKPRTRP 60
           MKDHLKTSEWGLGLKGHVIIAGPCSAETPEQVEKVCLEMKEQNIIPSMFRAGIWKPRTRP
Sbjct: 1   MKDHLKTSEWGLGLKGHVIIAGPCSAETPEQVEKVCLEMKEQNIIPSMFRAGIWKPRTRP 60

Query: 61  GSFEGIGEDGLKWMEIVRHHLNIPITTEVGNTAHVELALKHKVDVLWIGARTTVNPFAVQ 120
           GSFEGIGEDGLKWMEIVRHHLNIPITTEVGNTAHVELALKHKVDVLWIGARTTVNPFAVQ
Sbjct: 61  GSFEGIGEDGLKWMEIVRHHLNIPITTEVGNTAHVELALKHKVDVLWIGARTTVNPFAVQ 120

Query: 121 EIAEALKGTDIPVMVKNPMNPDLQLWIGALERLHAVGINKLAAIHRGFSDAYDKRFRNKP 180
           EIAEALKGTDIPVMVKNPMNPDLQLWIGALERLHAVGINKLAAIHRGFSDAYDKRFRNKP
Sbjct: 121 EIAEALKGTDIPVMVKNPMNPDLQLWIGALERLHAVGINKLAAIHRGFSDAYDKRFRNKP 180

Query: 181 NWSMPIHLKREWKGMEVINDPSHIVGKRDGILEISQRAINFGLDGLMIETHHDPDNAWSD 240
           NWSMPIHLKREWKGMEVINDPSHIVGKRDGILEISQRAINFGLDGLMIETHHDPDNAWSD
Sbjct: 181 NWSMPIHLKREWKGMEVINDPSHIVGKRDGILEISQRAINFGLDGLMIETHHDPDNAWSD 240

Query: 241 AKQQVTPAQLKDILSKIDFKTPLDSEKPSEKLHDLRSAIDHMDDQLIDLLAERFAVIDQI 300
           AKQQVTPAQLKDILSKIDFKTPLDSEKPSEKLHDLRSAIDHMDDQLIDLLAERFAVIDQI
Sbjct: 241 AKQQVTPAQLKDILSKIDFKTPLDSEKPSEKLHDLRSAIDHMDDQLIDLLAERFAVIDQI 300

Query: 301 GAHKREHKLTVFQSDRWKEVMDSRTDKGVKKGLSEKFMKELLFSIHEESVKRQEKQLRAG 360
           GAHKREHKLTVFQSDRWKEVMDSRTDKGVKKGLSEKFMKELLFSIHEESVKRQEKQLRAG
Sbjct: 301 GAHKREHKLTVFQSDRWKEVMDSRTDKGVKKGLSEKFMKELLFSIHEESVKRQEKQLRAG 360

Query: 361 DPVNKNA 367
           DPVNKNA
Sbjct: 361 DPVNKNA 367


Lambda     K      H
   0.318    0.135    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: 703
Number of extensions: 21
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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: 49 (23.5 bits)

Align candidate Echvi_0120 Echvi_0120 (3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase)
to HMM PF01817 (CM_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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.21344.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    1.6e-25   75.6   1.0    3.4e-25   74.6   1.0    1.6  1  lcl|FitnessBrowser__Cola:Echvi_0120  Echvi_0120 3-deoxy-D-arabino-hep


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0120  Echvi_0120 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   1.0   3.4e-25   3.4e-25       1      79 []     276     354 ..     276     354 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 3.4e-25
                                 CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifreiises 74 
                                          R+ Id++D++l++LlaeR++++++i++ K+e++l+v++ +R++ev++ ++++  ++gl+++++++++  i++es
  lcl|FitnessBrowser__Cola:Echvi_0120 276 RSAIDHMDDQLIDLLAERFAVIDQIGAHKREHKLTVFQSDRWKEVMDSRTDKGVKKGLSEKFMKELLFSIHEES 349
                                          899************************************************999******************** PP

                                 CM_2  75 ralQk 79 
                                          +++Q+
  lcl|FitnessBrowser__Cola:Echvi_0120 350 VKRQE 354
                                          ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (367 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: 8.45
//
[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