GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Magnetospirillum magneticum AMB-1

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011384000.1 AMB_RS08025 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>NCBI__GCF_000009985.1:WP_011384000.1
          Length = 362

 Score =  464 bits (1195), Expect = e-135
 Identities = 233/358 (65%), Positives = 280/358 (78%), Gaps = 8/358 (2%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GN  G LFR TTFGESHG A+GC+VDGVP  IPLTEAD+QH LD+R+PG +R+TTQRR
Sbjct: 1   MSGNGFGHLFRFTTFGESHGPAIGCVVDGVPARIPLTEADIQHYLDQRKPGQNRFTTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD+VKILSGVFEG+TTGTSIGLLIENTDQRS+DY  IKD +RPGHAD+ Y+QKYG+RDY
Sbjct: 61  EPDEVKILSGVFEGLTTGTSIGLLIENTDQRSKDYGEIKDTYRPGHADWVYQQKYGIRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYL-AEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177
           RGGGRSSARETAMRVAAGAIA+K L A   G+ IRG + QMG   +D    DW+++  NP
Sbjct: 121 RGGGRSSARETAMRVAAGAIARKVLDALAPGLSIRGAMVQMGPHAIDRSRWDWAELGNNP 180

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           F+CPD     + +E +  ++K G SIG  V VVASGVP GLG PV+D+LDAD+A A+MSI
Sbjct: 181 FWCPDGAAAKSWEEYLDTIRKSGSSIGGVVEVVASGVPVGLGAPVYDKLDADLAKAMMSI 240

Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQIIAHMAL 292
           NAVKGVEIGDGF   AL G +N DE+      + GF SNHAGGILGGIS+GQ ++  +A+
Sbjct: 241 NAVKGVEIGDGFAAAALSGEENADEMRMGNDGQVGFLSNHAGGILGGISTGQDVVVRLAV 300

Query: 293 KPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350
           KPTSSI  P ++++  G  VE+ TKGRHDPCV IRAVP+AEAM+A  L DHLLR  AQ
Sbjct: 301 KPTSSILTPKQSVDAKGNNVEVSTKGRHDPCVAIRAVPVAEAMMACTLADHLLRSLAQ 358


Lambda     K      H
   0.319    0.138    0.404 

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: 471
Number of extensions: 13
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: 361
Length of database: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_011384000.1 AMB_RS08025 (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.12440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.7e-140  451.6   0.0   9.8e-140  451.4   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384000.1  AMB_RS08025 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384000.1  AMB_RS08025 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.4   0.0  9.8e-140  9.8e-140       1     349 [.      10     357 ..      10     359 .. 0.98

  Alignments for each domain:
  == domain 1  score: 451.4 bits;  conditional E-value: 9.8e-140
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r+ttfGeSHg+a+g+++dG+Pa ++lte+diq++l++R+pgq r+t++r+E Dev+ilsGvfeG TtG
  lcl|NCBI__GCF_000009985.1:WP_011384000.1  10 FRFTTFGESHGPAIGCVVDGVPARIPLTEADIQHYLDQRKPGQNRFTTQRREPDEVKILSGVFEGLTTG 78 
                                               89******************************************************************* PP

                                 TIGR00033  70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138
                                               + i lli+N+d+rskdy +ik+++RPgHad++y++KYgi+d++gggrsSaReTa+rvaaGa+a+k L+ 
  lcl|NCBI__GCF_000009985.1:WP_011384000.1  79 TSIGLLIENTDQRSKDYGEIKDTYRPGHADWVYQQKYGIRDYRGGGRSSARETAMRVAAGAIARKVLDA 147
                                               *******************************************************************98 PP

                                 TIGR00033 139 ta.gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevv 206
                                                a g+ i + +v++g  +++++  +     +l ++p+ cpd  a+k  ee++d+++k+g s+Ggvvevv
  lcl|NCBI__GCF_000009985.1:WP_011384000.1 148 LApGLSIRGAMVQMGPHAIDRSRWDW---AELGNNPFWCPDGAAAKSWEEYLDTIRKSGSSIGGVVEVV 213
                                               6549****************988884...68899*********************************** PP

                                 TIGR00033 207 vsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsG 274
                                               +s+vpvglG p++dklda la+a++sinAvKgveiGdGF+aa   G e  De+ +  d+++ + +n+ G
  lcl|NCBI__GCF_000009985.1:WP_011384000.1 214 ASGVPVGLGAPVYDKLDADLAKAMMSINAVKGVEIGDGFAAAALSGEENADEMRMGnDGQVGFLSNHAG 282
                                               ******************************************************998999********* PP

                                 TIGR00033 275 GieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvlada 343
                                               Gi+GGi++G+d++vr avKp+++i +p+++vd ++++    tkgRhDpcv++ravpv+Eam+a +lad+
  lcl|NCBI__GCF_000009985.1:WP_011384000.1 283 GILGGISTGQDVVVRLAVKPTSSILTPKQSVDAKGNNVEVSTKGRHDPCVAIRAVPVAEAMMACTLADH 351
                                               **********************************99999999*************************** PP

                                 TIGR00033 344 llekra 349
                                               ll++ a
  lcl|NCBI__GCF_000009985.1:WP_011384000.1 352 LLRSLA 357
                                               **9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (362 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.31
//
[ok]

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

Links

Downloads

Related tools

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:

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