Alignments for a candidate for aroG in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Mesorhizobium ciceri WSM1271

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 YP_004143291.1 Mesci_4129 3-deoxy-7-phosphoheptulonate synthase

Query= SwissProt::A0A067XGX8
         (512 letters)



>NCBI__GCF_000185905.1:YP_004143291.1
          Length = 457

 Score =  542 bits (1396), Expect = e-158
 Identities = 264/445 (59%), Positives = 330/445 (74%), Gaps = 2/445 (0%)

Query: 60  TKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGNAF 119
           TKW+  SW+ KP  Q+P YPD   L++    L+T+PP+VFAGEAR L+++L   A G+AF
Sbjct: 2   TKWSPNSWRAKPIKQVPAYPDLAALKNTEAQLATFPPLVFAGEARKLKKQLASVAAGDAF 61

Query: 120 LLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 179
           LLQGGDCAESF E  A+NIRD FRV LQM VVL F G  PV+KVGR+AGQFAKPRS   E
Sbjct: 62  LLQGGDCAESFAEHGADNIRDFFRVFLQMSVVLTFAGAQPVVKVGRVAGQFAKPRSSDNE 121

Query: 180 EKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQRV 239
            K  V LPSYRGD +NG  FD KSRIPDP R   AY QS ATLNLLRAFA GGYA+++ V
Sbjct: 122 TKGEVTLPSYRGDIINGIEFDPKSRIPDPARQEMAYRQSAATLNLLRAFAQGGYASLENV 181

Query: 240 NQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD-HTIMTTTDFWTSHECLLLPY 298
           ++W L F   S QG++Y  LA+R+ E M FM A G+T + +  +  TDF+TSHE LLL Y
Sbjct: 182 HRWMLGFVSDSPQGEKYESLANRITETMDFMKAVGITSETNYALRETDFYTSHEALLLGY 241

Query: 299 EQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDELV 358
           E+ALTR DSTSG +Y  S HMIW+G+RTRQ D AHVE+ RGI NPLG+K    + PD L+
Sbjct: 242 EEALTRVDSTSGDWYATSGHMIWIGDRTRQPDHAHVEYCRGIKNPLGLKCGPSLTPDGLL 301

Query: 359 KLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKAPC 418
           +LID+LNP+N+PGR+T+I R G+D +   LP L+RAV+  G+ V W SDPMHGNT +A  
Sbjct: 302 ELIDLLNPENEPGRLTLIARFGSDKVADHLPKLVRAVQKEGRSVVWSSDPMHGNTIEA-A 360

Query: 419 GLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSRYH 478
           G KTR FD I  E++ FF+VH  EG++PGG+H+EMTG+NVTEC GG+R IT  +L  RYH
Sbjct: 361 GYKTRPFDRILKEVQTFFEVHRAEGTHPGGIHVEMTGKNVTECTGGARAITAEELQDRYH 420

Query: 479 THCDPRLNASQALELAFAIAERLRR 503
           THCDPRLNA QA+ELAF +++ L++
Sbjct: 421 THCDPRLNADQAIELAFLVSDLLKK 445


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: 680
Number of extensions: 21
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: 457
Length adjustment: 34
Effective length of query: 478
Effective length of database: 423
Effective search space:   202194
Effective search space used:   202194
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 YP_004143291.1 Mesci_4129 (3-deoxy-7-phosphoheptulonate synthase)
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.7811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-219  713.5   0.0   4.7e-219  713.3   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004143291.1  Mesci_4129 3-deoxy-7-phosphohept


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004143291.1  Mesci_4129 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.3   0.0  4.7e-219  4.7e-219       1     441 [.       4     445 ..       4     447 .. 0.99

  Alignments for each domain:
  == domain 1  score: 713.3 bits;  conditional E-value: 4.7e-219
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               ws++swr+kp +q+P yPd +al++++++l+++PPlv+age++klk++la va+G+afllqgGdcaesf
  lcl|NCBI__GCF_000185905.1:YP_004143291.1   4 WSPNSWRAKPIKQVPAYPDLAALKNTEAQLATFPPLVFAGEARKLKKQLASVAAGDAFLLQGGDCAESF 72 
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                                e  adnird +rv+lqm+vvlt+++  Pvvkvgr+aGq+akPrs++ e+k++vtlpsyrGd+ing +f
  lcl|NCBI__GCF_000185905.1:YP_004143291.1  73 AEHGADNIRDFFRVFLQMSVVLTFAGAQPVVKVGRVAGQFAKPRSSDNETKGEVTLPSYRGDIINGIEF 141
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               d ++r+pdp r   ay +saatlnllra+++gGya+l++vh+W l fv +sp+g++ye la++i+e++ 
  lcl|NCBI__GCF_000185905.1:YP_004143291.1 142 DPKSRIPDPARQEMAYRQSAATLNLLRAFAQGGYASLENVHRWMLGFVSDSPQGEKYESLANRITETMD 210
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm+avg+++++  al+++++ytshealll yeealtrvds++g+++ +s+h++WiG+rtrq d+ahve+
  lcl|NCBI__GCF_000185905.1:YP_004143291.1 211 FMKAVGITSETnyALRETDFYTSHEALLLGYEEALTRVDSTSGDWYATSGHMIWIGDRTRQPDHAHVEY 279
                                               *******9988789******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                                rg+knP+g+k+gps+++d ll+li+ l+PenePGrltli+r+G++k+a++lP+l++av+++Gr+vvW 
  lcl|NCBI__GCF_000185905.1:YP_004143291.1 280 CRGIKNPLGLKCGPSLTPDGLLELIDLLNPENEPGRLTLIARFGSDKVADHLPKLVRAVQKEGRSVVWS 348
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGnt+ea +Gyktr fd+il+ev++ffevh+aeGthpGG+h+e+tG++vtec+GGar+it ++l+
  lcl|NCBI__GCF_000185905.1:YP_004143291.1 349 SDPMHGNTIEA-AGYKTRPFDRILKEVQTFFEVHRAEGTHPGGIHVEMTGKNVTECTGGARAITAEELQ 416
                                               *********97.59******************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441
                                               +ry+t+cdPrlna+q++elaflv++ l++
  lcl|NCBI__GCF_000185905.1:YP_004143291.1 417 DRYHTHCDPRLNADQAIELAFLVSDLLKK 445
                                               ************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (457 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: 00:00:00.01
# Mc/sec: 10.29
//
[ok]

This GapMind analysis is from Apr 10 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