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

GapMind for Amino acid biosynthesis

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

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate Echvi_1518 Echvi_1518 chorismate synthase

Query= BRENDA::B5AAU3
         (442 letters)



>FitnessBrowser__Cola:Echvi_1518
          Length = 360

 Score =  420 bits (1080), Expect = e-122
 Identities = 211/352 (59%), Positives = 263/352 (74%), Gaps = 5/352 (1%)

Query: 55  GNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKET 114
           GN FG  F+++T+GESHG G+G +I GCP  +P+ E  ++ +L RR+PGQS+ITT RKE 
Sbjct: 2   GNSFGKVFKISTFGESHGKGLGVIIDGCPAGLPIDEAFIRQELQRRKPGQSKITTQRKEE 61

Query: 115 DTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQG 174
           D C+ILSG +EG +TGTPI + + NTDQ+  DY+ +A  YRPSHAD TY  K+GVR  +G
Sbjct: 62  DECQILSGVFEGKSTGTPIAIVIMNTDQKSKDYSHIADKYRPSHADYTYQEKFGVRDYRG 121

Query: 175 GGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIES 234
           GGRSSARET  RVAAGAVAK  LK   GVEI A+VS+   + L +    Y+ L   +IE 
Sbjct: 122 GGRSSARETAARVAAGAVAKLFLK-HIGVEINAYVSQAGHIKLDK---PYQELDFAEIEK 177

Query: 235 NICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAML 294
           NI RCPDPE AQ MID ID++R N +++GGVV+C+A+NVP GLG PVFD+L A L K+ML
Sbjct: 178 NIVRCPDPEVAQDMIDYIDEIRKNRDTVGGVVSCVAKNVPVGLGEPVFDRLHADLGKSML 237

Query: 295 SLPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKV 354
           S+ A KGFE GSGF G  + GSEHND FYMD G  VRT+TN SGG+QGGISNGE IYF+V
Sbjct: 238 SINAVKGFEYGSGFEGVTMLGSEHNDAFYMD-GDTVRTKTNHSGGIQGGISNGEDIYFRV 296

Query: 355 AFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMD 406
           AFKP ATI K Q++V +  + + +  +GRHDPCVVPRAVP+VE MAALVL D
Sbjct: 297 AFKPVATIMKDQDSVNQAGDQVTVSGKGRHDPCVVPRAVPIVEAMAALVLAD 348


Lambda     K      H
   0.317    0.135    0.396 

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: 457
Number of extensions: 18
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: 442
Length of database: 360
Length adjustment: 31
Effective length of query: 411
Effective length of database: 329
Effective search space:   135219
Effective search space used:   135219
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: 50 (23.9 bits)

Align candidate Echvi_1518 Echvi_1518 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.22328.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   8.2e-153  494.4   0.6   9.3e-153  494.2   0.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1518  Echvi_1518 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1518  Echvi_1518 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.2   0.6  9.3e-153  9.3e-153       1     348 [.       9     354 ..       9     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 494.2 bits;  conditional E-value: 9.3e-153
                            TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPial 74 
                                          +++ tfGeSHgk lg+iidG+Pagl+++e+ i++el+rR+pgqs+ t++rkEeDe +ilsGvfeGk tG+Pia+
  lcl|FitnessBrowser__Cola:Echvi_1518   9 FKISTFGESHGKGLGVIIDGCPAGLPIDEAFIRQELQRRKPGQSKITTQRKEEDECQILSGVFEGKSTGTPIAI 82 
                                          7899********************************************************************** PP

                            TIGR00033  75 likNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayv 148
                                          +i N+d++skdy++i++++RP+Hadyty++K+g++d++gggrsSaReTaarvaaGavak +Lk+  g+ei ayv
  lcl|FitnessBrowser__Cola:Echvi_1518  83 VIMNTDQKSKDYSHIADKYRPSHADYTYQEKFGVRDYRGGGRSSARETAARVAAGAVAKLFLKH-IGVEINAYV 155
                                          ****************************************************************.88******* PP

                            TIGR00033 149 vklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkl 222
                                          ++ g+++l++  ++e    +++k+ vrcpd+e ++ m ++id+++k++d+vGgvv++v++nvpvglGep+fd+l
  lcl|FitnessBrowser__Cola:Echvi_1518 156 SQAGHIKLDK-PYQELDFAEIEKNIVRCPDPEVAQDMIDYIDEIRKNRDTVGGVVSCVAKNVPVGLGEPVFDRL 228
                                          *********7.666678999****************************************************** PP

                            TIGR00033 223 daelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpip 296
                                          +a l++ +lsinAvKg+e G+GFe +++ Gse+nD ++++ d +r+ktn+sGGi+GGi+nGedi++r+a+Kp++
  lcl|FitnessBrowser__Cola:Echvi_1518 229 HADLGKSMLSINAVKGFEYGSGFEGVTMLGSEHNDAFYMDGDTVRTKTNHSGGIQGGISNGEDIYFRVAFKPVA 302
                                          ************************************************************************** PP

                            TIGR00033 297 tikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekr 348
                                          ti k++ +v+ ++ + +   kgRhDpcvvpravp+vEam alvlad +l kr
  lcl|FitnessBrowser__Cola:Echvi_1518 303 TIMKDQDSVNQAGDQVTVSGKGRHDPCVVPRAVPIVEAMAALVLADFVLLKR 354
                                          ***********888888888***************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (360 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: 00:00:00.01
# Mc/sec: 12.19
//
[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