Alignments for a candidate for cmutase in Marinobacter adhaerens HP15

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.11296.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.27
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis