Alignments for a candidate for aroG in Marivita geojedonensis DPG-138

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Marivita geojedonensis DPG-138

Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate WP_085639197.1 MGEO_RS14420 3-deoxy-7-phosphoheptulonate synthase class II

Query= SwissProt::A0A067XGX8
         (512 letters)



>NCBI__GCF_002115805.1:WP_085639197.1
          Length = 456

 Score =  538 bits (1385), Expect = e-157
 Identities = 262/447 (58%), Positives = 335/447 (74%), Gaps = 2/447 (0%)

Query: 60  TKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNAF 119
           T+W    W+ KP  Q+P+Y D+ +LE+V   LS YPP+VFAGEAR L++ LG A+ G AF
Sbjct: 2   TEWQKSGWRAKPRVQMPEYTDQAKLEAVEAQLSKYPPLVFAGEARKLKKALGAASRGEAF 61

Query: 120 LLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 179
           LLQGGDCAE+F +FSAN+IRDTF+VMLQM +VL FG ++PV+KVGRMAGQFAKPRS P E
Sbjct: 62  LLQGGDCAEAFDQFSANSIRDTFKVMLQMAMVLTFGAKVPVVKVGRMAGQFAKPRSAPTE 121

Query: 180 EKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQRV 239
             DGV+LPSYRGD +N  AF  ++RIPDP +M++AYTQ+ ATLNLLRAF++GGYA + +V
Sbjct: 122 VVDGVELPSYRGDIINELAFTPEARIPDPAKMLQAYTQAAATLNLLRAFSTGGYADVHQV 181

Query: 240 NQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVDHT-IMTTTDFWTSHECLLLPY 298
           +QW L FTD+ E+ ++YR++A+R+ + + FM AAGL  D    + T DF+TSHE LLL Y
Sbjct: 182 HQWTLGFTDR-EESEKYRDMANRISDTLDFMKAAGLDSDREPSLQTVDFYTSHESLLLEY 240

Query: 299 EQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDELV 358
           E+ALTR+DSTSG +   S HMIW+G+RTRQ DGAHVEF RG+ NP+G+K       ++L 
Sbjct: 241 EEALTRQDSTSGKWLAGSGHMIWIGDRTRQPDGAHVEFARGVLNPVGLKCGPTTTAEDLK 300

Query: 359 KLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAPC 418
            L+  LNP+N+ G++T+I R GA  +   LP LI+ V   G  VTWV DPMHGNT K+  
Sbjct: 301 VLMAKLNPENEAGKLTLIARFGAGKVAEHLPRLIKTVAEEGANVTWVCDPMHGNTIKSST 360

Query: 419 GLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRYH 478
           G KTR FD++  E++ FF VH  EG+ PGGVH EMTGQ+VTEC GG R ++  DLS RYH
Sbjct: 361 GYKTRPFDAVLREVKEFFAVHNAEGTVPGGVHFEMTGQDVTECTGGVRAVSEEDLSDRYH 420

Query: 479 THCDPRLNASQALELAFAIAERLRRRR 505
           T CDPRLNASQ+LELAF +AE L  RR
Sbjct: 421 TACDPRLNASQSLELAFLVAEELTSRR 447


Lambda     K      H
   0.319    0.134    0.401 

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: 637
Number of extensions: 22
Number of successful extensions: 3
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: 512
Length of database: 456
Length adjustment: 34
Effective length of query: 478
Effective length of database: 422
Effective search space:   201716
Effective search space used:   201716
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: 52 (24.6 bits)

Align candidate WP_085639197.1 MGEO_RS14420 (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.2809568.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-213  695.3   0.0   1.6e-213  695.0   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085639197.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085639197.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.0   0.0  1.6e-213  1.6e-213       1     442 [.       4     446 ..       4     447 .. 0.99

  Alignments for each domain:
  == domain 1  score: 695.0 bits;  conditional E-value: 1.6e-213
                             TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeve 73 
                                           w+++ wr+kp +q+Pey d+++leav+++l+++PPlv+age++klk+ l+++++GeafllqgGdcae+f++++
  NCBI__GCF_002115805.1:WP_085639197.1   4 WQKSGWRAKPRVQMPEYTDQAKLEAVEAQLSKYPPLVFAGEARKLKKALGAASRGEAFLLQGGDCAEAFDQFS 76 
                                           77889******************************************************************** PP

                             TIGR01358  74 adnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpd 146
                                           a++ird+++v+lqma+vlt+ga++Pvvkvgr+aGq+akPrs+p+e+ dgv+lpsyrGd+in  af+ +ar+pd
  NCBI__GCF_002115805.1:WP_085639197.1  77 ANSIRDTFKVMLQMAMVLTFGAKVPVVKVGRMAGQFAKPRSAPTEVVDGVELPSYRGDIINELAFTPEARIPD 149
                                           ************************************************************************* PP

                             TIGR01358 147 perlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae. 218
                                           p ++++ay+++aatlnllra+ +gGyad+++vh+W+l f+ + +++++y+++a++i+++l fm+a+g+++++ 
  NCBI__GCF_002115805.1:WP_085639197.1 150 PAKMLQAYTQAAATLNLLRAFSTGGYADVHQVHQWTLGFTDR-EESEKYRDMANRISDTLDFMKAAGLDSDRe 221
                                           ***************************************987.56799********************99887 PP

                             TIGR01358 219 .alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsm 290
                                            +l++v++ytshe+lll+yeealtr+ds++g++   s+h++WiG+rtrq dgahvef+rgv nP+g+k+gp++
  NCBI__GCF_002115805.1:WP_085639197.1 222 pSLQTVDFYTSHESLLLEYEEALTRQDSTSGKWLAGSGHMIWIGDRTRQPDGAHVEFARGVLNPVGLKCGPTT 294
                                           99*********************************************************************** PP

                             TIGR01358 291 eadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrf 363
                                           +a++l  l+ +l+Pene G+ltli+r+Ga k+ae+lP+l++ v ++G++v+Wv+dpmhGnt+++++Gyktr f
  NCBI__GCF_002115805.1:WP_085639197.1 295 TAEDLKVLMAKLNPENEAGKLTLIARFGAGKVAEHLPRLIKTVAEEGANVTWVCDPMHGNTIKSSTGYKTRPF 367
                                           ************************************************************************* PP

                             TIGR01358 364 ddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflva 436
                                           d++l evkeff+vh+aeGt pGGvh e+tG+dvtec+GG r+++e+dl++ry+tacdPrlna+qslelaflva
  NCBI__GCF_002115805.1:WP_085639197.1 368 DAVLREVKEFFAVHNAEGTVPGGVHFEMTGQDVTECTGGVRAVSEEDLSDRYHTACDPRLNASQSLELAFLVA 440
                                           ************************************************************************* PP

                             TIGR01358 437 eklrea 442
                                           e l ++
  NCBI__GCF_002115805.1:WP_085639197.1 441 EELTSR 446
                                           *98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (456 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.80
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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