GapMind for Amino acid biosynthesis

 

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

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011383631.1 AMB_RS06190 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000009985.1:WP_011383631.1
          Length = 462

 Score =  586 bits (1510), Expect = e-172
 Identities = 287/445 (64%), Positives = 344/445 (77%), Gaps = 1/445 (0%)

Query: 75  WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134
           W+PESW+ K   Q P YP++ +L  V +++  FPP+VFAGEAR L+  LAD A GKAFLL
Sbjct: 5   WSPESWRAKPIHQAPTYPDSAKLAEVEESLRNFPPLVFAGEARRLKASLADVADGKAFLL 64

Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194
           QGGDCAESF EF+A NIRDTFRVLLQM++VLT+G  +PV+KVGRMAGQFAKPRS   E  
Sbjct: 65  QGGDCAESFAEFHANNIRDTFRVLLQMAVVLTYGAAMPVVKVGRMAGQFAKPRSADTETI 124

Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254
           DGV LPSY+GDN+NG  F  ++R+PDP RMIRAY QSAATLNLLRAFA GGYA + +V Q
Sbjct: 125 DGVTLPSYRGDNVNGSEFTAEARVPDPLRMIRAYNQSAATLNLLRAFAQGGYADLHKVHQ 184

Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTDH-PLMTTTDFYTSHECLLLPYEQ 313
           W L  V  + QA RYQ+L +R+DE L FM ACG+ +D  P +  TDF+TSHE LL+PYEQ
Sbjct: 185 WTLGCVAGTLQAARYQDLCDRLDETLAFMEACGMTSDTTPQLRETDFFTSHEALLMPYEQ 244

Query: 314 SLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVKL 373
           +LTR+DST+G +YDCSAHM+W GERTRQ+D  HVEFLRG+ NPLG K    M P +L++L
Sbjct: 245 ALTRIDSTTGDWYDCSAHMLWIGERTRQMDAGHVEFLRGVKNPLGFKAGPGMSPDDLLRL 304

Query: 374 VEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCGL 433
           ++ LNP N+ GRITVI RMGAE +   LP LIRAV R G+ V W CDPMH NTIKA  G 
Sbjct: 305 IDRLNPENESGRITVITRMGAEKVEQVLPGLIRAVEREGRKVVWSCDPMHANTIKAAGGY 364

Query: 434 KTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHTH 493
           KTR FD+ILAEVRAF  VH+ EGSHAGG+H EMTGQ+VTECIGG   V  +DL  RY T 
Sbjct: 365 KTRPFDAILAEVRAFFAVHKAEGSHAGGVHFEMTGQDVTECIGGMTGVAEEDLGDRYQTA 424

Query: 494 CDPRLNASQSLELAFIVAERLRKRR 518
           CDPRLNA+QSLELAF++AE+L+  R
Sbjct: 425 CDPRLNATQSLELAFLIAEQLKDER 449


Lambda     K      H
   0.318    0.132    0.389 

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: 675
Number of extensions: 19
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: 525
Length of database: 462
Length adjustment: 34
Effective length of query: 491
Effective length of database: 428
Effective search space:   210148
Effective search space used:   210148
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: 52 (24.6 bits)

Align candidate WP_011383631.1 AMB_RS06190 (3-deoxy-7-phosphoheptulonate synthase class II)
to HMM TIGR01358 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.474.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-224  730.2   0.0   3.9e-224  730.0   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383631.1  AMB_RS06190 3-deoxy-7-phosphohep


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383631.1  AMB_RS06190 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.0   0.0  3.9e-224  3.9e-224       1     442 [.       5     448 ..       5     449 .. 0.99

  Alignments for each domain:
  == domain 1  score: 730.0 bits;  conditional E-value: 3.9e-224
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               ws+eswr+kp  q P+yPd+++l +v+++l+++PPlv+age+++lk++la+va G+afllqgGdcaesf
  lcl|NCBI__GCF_000009985.1:WP_011383631.1   5 WSPESWRAKPIHQAPTYPDSAKLAEVEESLRNFPPLVFAGEARRLKASLADVADGKAFLLQGGDCAESF 73 
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                                e++a+nird++rvllqmavvltyga +Pvvkvgr+aGq+akPrs+++e+ dgvtlpsyrGd++ng +f
  lcl|NCBI__GCF_000009985.1:WP_011383631.1  74 AEFHANNIRDTFRVLLQMAVVLTYGAAMPVVKVGRMAGQFAKPRSADTETIDGVTLPSYRGDNVNGSEF 142
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               +++arvpdp r++ray++saatlnllra+++gGyadl+kvh+W+l  v  + ++ary++l++++de+l 
  lcl|NCBI__GCF_000009985.1:WP_011383631.1 143 TAEARVPDPLRMIRAYNQSAATLNLLRAFAQGGYADLHKVHQWTLGCVAGTLQAARYQDLCDRLDETLA 211
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm+a+g+++++  +l++++++tsheall++ye+altr ds++g+++d+sah+lWiGertrq+d  hvef
  lcl|NCBI__GCF_000009985.1:WP_011383631.1 212 FMEACGMTSDTtpQLRETDFFTSHEALLMPYEQALTRIDSTTGDWYDCSAHMLWIGERTRQMDAGHVEF 280
                                               *******9998899******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                               lrgvknP+g k gp m++d+ll+li++l+Pene Gr+t+i+r+Gaek+ + lP l++av+++Gr+vvW 
  lcl|NCBI__GCF_000009985.1:WP_011383631.1 281 LRGVKNPLGFKAGPGMSPDDLLRLIDRLNPENESGRITVITRMGAEKVEQVLPGLIRAVEREGRKVVWS 349
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmh nt++aa+Gyktr fd+il+ev++ff+vhkaeG+h GGvh e+tG+dvtec+GG   ++e+dl 
  lcl|NCBI__GCF_000009985.1:WP_011383631.1 350 CDPMHANTIKAAGGYKTRPFDAILAEVRAFFAVHKAEGSHAGGVHFEMTGQDVTECIGGMTGVAEEDLG 418
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklrea 442
                                               +ry+tacdPrlna qslelafl+ae+l+++
  lcl|NCBI__GCF_000009985.1:WP_011383631.1 419 DRYQTACDPRLNATQSLELAFLIAEQLKDE 448
                                               ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (462 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.00
//
[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:

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