Alignments for a candidate for cmutase in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Dechlorosoma suillum PS

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 Dsui_1940 Dsui_1940 chorismate mutase, clade 2

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__PS:Dsui_1940
          Length = 374

 Score =  386 bits (991), Expect = e-112
 Identities = 192/360 (53%), Positives = 254/360 (70%), Gaps = 6/360 (1%)

Query: 7   LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66
           L  +R+ ID++D ++LDL++ RARCAQ+V  +K       +    YRPEREA VL+ I +
Sbjct: 18  LSVVRMDIDAIDAQLLDLLNRRARCAQQVGEIKARH---GDAGFIYRPEREAQVLRRIQD 74

Query: 67  LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126
           +N+GPL +E +   FRE+MS+CL+LEQPL +A+LGP GTFS++A+ KHFGH+    P A+
Sbjct: 75  MNQGPLSSESVTWFFREVMSACLSLEQPLGIAFLGPLGTFSESASTKHFGHAARLLPQAS 134

Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186
           ID+VFREV AG  N+GV PVENSTEGAV  TLD  L   + ICGEV LRIH HLL  +  
Sbjct: 135 IDDVFREVEAGHANYGVAPVENSTEGAVGRTLDLLLGTSLKICGEVVLRIHQHLLT-KAP 193

Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246
             DR+T++YSHAQSLAQC +WL+ H PNV R++V SNA AA+    E  +AAIAG+ AA 
Sbjct: 194 SLDRVTKVYSHAQSLAQCHEWLNRHLPNVPRISVGSNAQAAQMAAQEEGAAAIAGEAAAD 253

Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPT--GDDKTSIIVSMRNKPGALHELLMPFH 304
            Y L +LAE IED P N+TRF+++G  +  P+  G DKTS+I+S+ N  GALH LL+PF 
Sbjct: 254 RYDLPRLAESIEDEPNNTTRFVVLGRHDAGPSTAGKDKTSLIMSIPNNTGALHTLLVPFA 313

Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364
             G+ LTR+E+RP+R   W YVFF+D  GH  +P +K  L+++   A  LKVLGSYP AV
Sbjct: 314 DAGVSLTRLESRPARHTLWEYVFFVDVDGHRDEPRVKAALDELARRAAYLKVLGSYPVAV 373


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: 375
Number of extensions: 16
Number of successful extensions: 4
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: 374
Length adjustment: 30
Effective length of query: 335
Effective length of database: 344
Effective search space:   115240
Effective search space used:   115240
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 Dsui_1940 Dsui_1940 (chorismate mutase, clade 2)
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.5139.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.5e-34  104.4   0.1    2.1e-33  100.8   0.1    2.3  2  lcl|FitnessBrowser__PS:Dsui_1940  Dsui_1940 chorismate mutase, cla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1940  Dsui_1940 chorismate mutase, clade 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.1   2.1e-33   2.1e-33       2      76 .]      19      93 ..      18      93 .. 0.97
   2 ?    0.9   0.0      0.03      0.03      62      75 ..     129     142 ..     120     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 2.1e-33
                         TIGR01807  2 kelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavarifrEim 76
                                        +R  iDaiD+++ldLl+ Ra++a++vge+K +  + ++iYRPeREa+vlrr++++n+GpL +e+v   frE+m
  lcl|FitnessBrowser__PS:Dsui_1940 19 SVVRMDIDAIDAQLLDLLNRRARCAQQVGEIKARHGDAGFIYRPEREAQVLRRIQDMNQGPLSSESVTWFFREVM 93
                                      56899*********************************************************************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.03
                         TIGR01807  62 pLdqeavarifrEi 75 
                                       +L+q +++ +frE+
  lcl|FitnessBrowser__PS:Dsui_1940 129 LLPQASIDDVFREV 142
                                       799**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (76 nodes)
Target sequences:                          1  (374 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: 8.03
//
[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:

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