GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Marinobacter adhaerens HP15

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate GFF1395 HP15_1362 chorismate mutase / prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__Marino:GFF1395
          Length = 365

 Score =  464 bits (1195), Expect = e-135
 Identities = 235/363 (64%), Positives = 280/363 (77%), Gaps = 1/363 (0%)

Query: 3   EADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLK 62
           E  +L  LR  ID LD++I++LIS RA CAQEVA VK  + P  ++  FYRPEREA VL+
Sbjct: 4   EQVRLGELRDEIDQLDQKIMELISARAACAQEVAHVKMTANP-GQDVFFYRPEREAQVLR 62

Query: 63  HIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISK 122
            I E N GPL  EEMARLFREIMS+CLALE+P+ +A+LGP GTF+QAAALKHFGHSV+S 
Sbjct: 63  RIKEQNPGPLSGEEMARLFREIMSACLALEKPMHIAFLGPIGTFTQAAALKHFGHSVVSV 122

Query: 123 PMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLV 182
           P+ AID VFREV +GA ++GVVPVENSTEG +NHTLD F+   + ICGEV+LRIHHHLLV
Sbjct: 123 PLPAIDAVFREVESGAAHYGVVPVENSTEGMINHTLDMFMSSPLKICGEVQLRIHHHLLV 182

Query: 183 GETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGD 242
                   ITRIYSH QS AQCR+WLD H   +ERV VSSNA+AA+R   E  +AAIAGD
Sbjct: 183 SPKHGDQEITRIYSHQQSFAQCRQWLDTHRYGIERVTVSSNAEAARRAAEEPGTAAIAGD 242

Query: 243 MAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMP 302
           MAA+LYGL KLA  IEDRP N+TRFLIIG +EVP +G DK+SI+VSMRNKPGAL++LL P
Sbjct: 243 MAAELYGLQKLANSIEDRPDNTTRFLIIGREEVPASGHDKSSILVSMRNKPGALYQLLEP 302

Query: 303 FHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362
           FH +G+ LTRIETRPS SG W YVF+ID  GH +D  ++ VL ++  EAV LK LGSYP 
Sbjct: 303 FHRHGLSLTRIETRPSPSGTWAYVFYIDFEGHMEDEQVRKVLAEVDEEAVELKRLGSYPI 362

Query: 363 AVL 365
            VL
Sbjct: 363 GVL 365


Lambda     K      H
   0.319    0.133    0.390 

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: 401
Number of extensions: 10
Number of successful extensions: 2
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate GFF1395 HP15_1362 (chorismate mutase / prephenate dehydratase)
to HMM TIGR01807 (pheA: 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/TIGR01807.hmm
# target sequence database:        /tmp/gapView.32011.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01807  [M=76]
Accession:   TIGR01807
Description: CM_P2: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.4e-33  100.1   0.3    1.3e-32   98.2   0.2    2.0  2  lcl|FitnessBrowser__Marino:GFF1395  HP15_1362 chorismate mutase / pr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1395  HP15_1362 chorismate mutase / prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.2   1.3e-32   1.3e-32       1      76 []       8      85 ..       8      85 .. 0.95
   2 ?   -2.3   0.0      0.31      0.31      67      75 ..     126     134 ..     122     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.3e-32
                           TIGR01807  1 LkelRnkiDaiDdrildLlseRaklakavgelKkks..aseaviYRPeREaavlrrlkelnkGpLdqeavarifrEi 75
                                        L elR++iD +D++i++L+s Ra +a++v+++K ++   ++ ++YRPeREa+vlrr+ke+n+GpL  e++ar+frEi
  lcl|FitnessBrowser__Marino:GFF1395  8 LGELRDEIDQLDQKIMELISARAACAQEVAHVKMTAnpGQDVFFYRPEREAQVLRRIKEQNPGPLSGEEMARLFREI 84
                                        679******************************9976567789********************************** PP

                           TIGR01807 76 m 76
                                        m
  lcl|FitnessBrowser__Marino:GFF1395 85 M 85
                                        9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.31
                           TIGR01807  67 avarifrEi 75 
                                         a++++frE+
  lcl|FitnessBrowser__Marino:GFF1395 126 AIDAVFREV 134
                                         79999**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 nodes)
Target sequences:                          1  (365 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: 12.58
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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