Alignments for a candidate for cmutase in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Persephonella marina EX-H1

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 WP_012675980.1 PERMA_RS01125 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000021565.1:WP_012675980.1
          Length = 361

 Score =  293 bits (750), Expect = 5e-84
 Identities = 156/366 (42%), Positives = 232/366 (63%), Gaps = 9/366 (2%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           M    +L+ LR +ID +DE+IL L++ERA+ AQEV  +K     K      Y P RE  +
Sbjct: 1   MDYKKKLEELRNKIDQIDEQILRLLNERAKLAQEVGHIK-----KEHNLPIYVPSREKAI 55

Query: 61  LKHIMELNK--GPL-DNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGH 117
            + + +LN   G +   + +  +FREI+S+C + E+ ++VAYLGP  TF+  AA+KHFG 
Sbjct: 56  FERLEKLNAELGEIFPTDAVKPVFREIISACRSTEESIKVAYLGPRATFTHQAAIKHFGQ 115

Query: 118 SVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIH 177
           +V   P++ I +VF E+V    +FGVVPVEN+ EG VN+TLD  +++ + I GEV L I 
Sbjct: 116 AVEHIPVSTIKDVFEEIVKEKADFGVVPVENTIEGIVNYTLDLLVDYPLKITGEVILEIS 175

Query: 178 HHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSA 237
            HL+ G       I R+YSH  +LA+CR WL  + PN + + V S A AA+  K ++ SA
Sbjct: 176 LHLM-GINPDVREIVRVYSHRHALAECRDWLRENLPNAQLIEVESTAKAAEMAKDDYESA 234

Query: 238 AIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALH 297
           A+A + AA +YGL  +  KI+    N TRFL+IG+Q    TG+DKT+ I S++N+ GAL+
Sbjct: 235 AVASEAAADIYGLHIIERKIDRHIHNFTRFLVIGTQIPNRTGNDKTTFIFSVKNEVGALY 294

Query: 298 ELLMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVL 357
           + L P + +GI++T+IE+RPS+   W Y+FF D  GH QD  ++  L+++   +   K+L
Sbjct: 295 KTLEPLYRHGINMTKIESRPSKKEAWDYIFFTDIEGHIQDERVEKALKELEEISPFFKIL 354

Query: 358 GSYPKA 363
           GSYPKA
Sbjct: 355 GSYPKA 360


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: 341
Number of extensions: 13
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: 365
Length of database: 361
Length adjustment: 29
Effective length of query: 336
Effective length of database: 332
Effective search space:   111552
Effective search space used:   111552
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 WP_012675980.1 PERMA_RS01125 (prephenate dehydratase)
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.24297.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.7e-30   90.9   2.0    3.3e-29   87.5   0.7    2.7  2  lcl|NCBI__GCF_000021565.1:WP_012675980.1  PERMA_RS01125 prephenate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012675980.1  PERMA_RS01125 prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.7   3.3e-29   3.3e-29       1      78 [.      11      90 ..      11      91 .. 0.93
   2 ?    1.5   0.0     0.021     0.021      55      73 ..     117     135 ..     105     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 3.3e-29
                                      CM_2  1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre.gaeel..gldpeavekifr 68
                                              R++Id+iD+++l+Ll+eR++la+e++++Kke++lp++ p+Re++++erl++ + +el   ++ +av+ +fr
  lcl|NCBI__GCF_000021565.1:WP_012675980.1 11 RNKIDQIDEQILRLLNERAKLAQEVGHIKKEHNLPIYVPSREKAIFERLEKlN-AELgeIFPTDAVKPVFR 80
                                              99*************************************************63.45434799********* PP

                                      CM_2 69 eiisesralQ 78
                                              eiis++r+ +
  lcl|NCBI__GCF_000021565.1:WP_012675980.1 81 EIISACRSTE 90
                                              *******988 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.021
                                      CM_2  55 elgldpeavekifreiise 73 
                                                ++++ ++++++f+ei++e
  lcl|NCBI__GCF_000021565.1:WP_012675980.1 117 VEHIPVSTIKDVFEEIVKE 135
                                               4679999*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (361 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: 8.42
//
[ok]

This GapMind analysis is from Apr 10 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:

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
the source code
instructions for running GapMind on your computer
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