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

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.10068.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.62
//
[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