Alignments for a candidate for aroG in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012408002.1 NPUN_RS06410 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_000020025.1:WP_012408002.1
          Length = 366

 Score =  300 bits (769), Expect = 3e-86
 Identities = 167/337 (49%), Positives = 225/337 (66%), Gaps = 13/337 (3%)

Query: 1   MIVVLKPGSTEEDIRKVVK-LAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDC- 58
           MI++LK G+  E+I ++ + L+E++ +    S G  + V+G+IGD   +  DK +  +  
Sbjct: 1   MIIILKNGTPAEEITRISQELSETWKVTVEKSIGTHKVVLGLIGDTTSI--DKLQIQEYS 58

Query: 59  --VESVVRVLKPYKLVSREF-HPEDTVIDL----GDVKIGNGY-FTIIAGPCSVEGREML 110
             +E V+RV +P+K VSREF H E + + +    GDV  G  +   ++AGPCSVE   M+
Sbjct: 59  PWIEQVLRVQQPFKRVSREFRHGEASEVVVPTPNGDVYFGEHHPIVVVAGPCSVENEAMI 118

Query: 111 METAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDD 170
           +ETA  +   G K LRGGAYKPRTSPY+FQG GE  L+ L  A +  G+ +VTE +   D
Sbjct: 119 VETAKRVKAAGAKFLRGGAYKPRTSPYAFQGYGESALDLLAAAREATGLGIVTELMDAAD 178

Query: 171 LPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNT 230
           L  VA  ADIIQIGARN  NF LL K G+ +KPVLLKRG   TI+E+L++AEYI  SGN 
Sbjct: 179 LSAVARTADIIQIGARNMHNFSLLKKVGAQDKPVLLKRGMSATIDEWLMAAEYILASGNP 238

Query: 231 KIILCERGIRTFE-KATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIA 289
            +ILCERGIRTF+ K  RNTLD+S +P++R  +HLPI++DPSH  GR + V  ++ AAIA
Sbjct: 239 NVILCERGIRTFDGKYARNTLDLSVLPVLRSLTHLPIMIDPSHGTGRSEYVPSMAIAAIA 298

Query: 290 VGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEM 326
            G   +++EVHP P KALSDG QSL  + F  LVQEM
Sbjct: 299 AGTDSLMIEVHPNPAKALSDGPQSLTPDKFDRLVQEM 335


Lambda     K      H
   0.318    0.138    0.388 

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: 318
Number of extensions: 11
Number of successful extensions: 5
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: 338
Length of database: 366
Length adjustment: 29
Effective length of query: 309
Effective length of database: 337
Effective search space:   104133
Effective search space used:   104133
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: 49 (23.5 bits)

Align candidate WP_012408002.1 NPUN_RS06410 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01361 (aroF: 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/TIGR01361.hmm
# target sequence database:        /tmp/gapView.3482804.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01361  [M=260]
Accession:   TIGR01361
Description: DAHP_synth_Bsub: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-123  396.6   0.0   2.8e-123  396.4   0.0    1.1  1  NCBI__GCF_000020025.1:WP_012408002.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012408002.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.4   0.0  2.8e-123  2.8e-123       3     259 ..      74     337 ..      72     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 396.4 bits;  conditional E-value: 2.8e-123
                             TIGR01361   3 askkvkkeetvvdved.....vkiGege.liviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 
                                           +s+++++ e+ + v       v +Ge + ++v+aGPCsve+e +ivetak+vk+aGak+lrGga+kPrtsPy+
  NCBI__GCF_000020025.1:WP_012408002.1  74 VSREFRHGEASEVVVPtpngdVYFGEHHpIVVVAGPCSVENEAMIVETAKRVKAAGAKFLRGGAYKPRTSPYA 146
                                           6777776655444422222349*****967789**************************************** PP

                             TIGR01361  70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrgla 142
                                           fqG+ge++l ll++a+++tgl +vte++d++d++ va+ +Di+qiGarnm+nf+lLk+vg+++kPvlLkrg++
  NCBI__GCF_000020025.1:WP_012408002.1 147 FQGYGESALDLLAAAREATGLGIVTELMDAADLSAVARTADIIQIGARNMHNFSLLKKVGAQDKPVLLKRGMS 219
                                           ************************************************************************* PP

                             TIGR01361 143 atieewleaaeYilsegnenvilcerGirtfe.katrftldlsavallkklthlPvivDpshaaGrrdlvlpl 214
                                           ati+ewl+aaeYil++gn+nvilcerGirtf+ k++r+tldls++++l++lthlP+++Dpsh++Gr+++v+++
  NCBI__GCF_000020025.1:WP_012408002.1 220 ATIDEWLMAAEYILASGNPNVILCERGIRTFDgKYARNTLDLSVLPVLRSLTHLPIMIDPSHGTGRSEYVPSM 292
                                           ********************************99*************************************** PP

                             TIGR01361 215 akaavavGadgllievhpdPekalsDseqqltpeefkelvkelka 259
                                           a aa+a+G+d+l+ievhp+P+kalsD++q+ltp++f++lv+e+++
  NCBI__GCF_000020025.1:WP_012408002.1 293 AIAAIAAGTDSLMIEVHPNPAKALSDGPQSLTPDKFDRLVQEMSI 337
                                           *****************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (366 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.88
//
[ok]

This GapMind analysis is from Jul 25 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 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