Alignments for a candidate for aroG in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Pseudarthrobacter sulfonivorans Ar51

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_058929394.1 AU252_RS02595 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::O68903
         (455 letters)



>NCBI__GCF_001484605.1:WP_058929394.1
          Length = 464

 Score =  504 bits (1298), Expect = e-147
 Identities = 250/438 (57%), Positives = 314/438 (71%), Gaps = 6/438 (1%)

Query: 19  LDDALGRPAAQQPEWPDADLARRVRAVLESVPPITVPAEIDRLRENLAAVARGEAFMLQG 78
           LDD    P +QQP W D D+       L  +PP+    E+D LRE LAA A G+AF+LQG
Sbjct: 27  LDDWRDLPVSQQPSWQDKDVFDASLGELSVLPPLVFAGEVDVLRERLAAAAEGKAFLLQG 86

Query: 79  GDCAETFADNTEPHIRANVRTLLQMAVVLTYGASLPVVKIGRIAGQYAKPRSSGT---DA 135
           GDCAETF   T   I A V+T+LQMAVVLTYGA++PV+K+GR+AGQ+AKPRSS     D 
Sbjct: 87  GDCAETFEAATADKISARVKTILQMAVVLTYGAAMPVIKMGRMAGQFAKPRSSNDETRDG 146

Query: 136 LGLPSYRGDIVNSLVPTPEARVADPGRMIRAYANAGAAMNLLRAMTTAGMADLHRLHDWN 195
           + LP+YRGDIVN    TPE+R  D  RM++AY  + + +NL+RA T  G ADL  +H WN
Sbjct: 147 VTLPAYRGDIVNGYEFTPESRGHDAARMLKAYHTSASTLNLIRAFTQGGFADLRSVHQWN 206

Query: 196 KDFVRTSPAGERYEALAAEIDRGLRFMSACGVNDSSLHTTEIFASHEALLLDYERALLRL 255
           K F   +PA  RYE+LA +IDR ++FM++CG +  +L   E FASHEALLLDYERAL R+
Sbjct: 207 KGFTE-NPAHARYESLARDIDRAIKFMASCGADFEALKRVEFFASHEALLLDYERALTRI 265

Query: 256 DTRGDEPKLYDLSSHFLWIGERTKQLDGAHIAFAELLANPIGLKIGPSTTPEMAVEYVER 315
           D+R   P  YD S+HFLWIGERT++LD AH+ F   + NPIG+K+GPSTT + A+  +++
Sbjct: 266 DSRTGFP--YDTSAHFLWIGERTRELDHAHVDFLSRVRNPIGVKLGPSTTGDDALRLIDK 323

Query: 316 LDPHNQPGRLTLIIRMGNGKVRDVLPAIVEKVTASGHKVIWQCDPMHGNTHESSTGYKTR 375
           LDP  +PGRLT I RMG G +R+ LPAIVEKVTASG KV+W  DPMHGNT  S  GYKTR
Sbjct: 324 LDPEREPGRLTFITRMGAGNIREKLPAIVEKVTASGAKVLWVTDPMHGNTVTSPNGYKTR 383

Query: 376 HFDRIVDEVQGFFEVHRRLGTHPGGIHIELTGEDVTECLGGAQEISDTDLAGRYETACDP 435
           +FD ++DEV+GFFEVH  LGT PGG+H+E+TG+DV ECLGGA  +       +YE+ CDP
Sbjct: 384 NFDDVIDEVRGFFEVHHALGTVPGGLHVEMTGDDVAECLGGADPVDQEAFLDKYESVCDP 443

Query: 436 RLNTQQSLELAFLVAEML 453
           RLN  QSLE+AFLVA  L
Sbjct: 444 RLNHMQSLEMAFLVAGAL 461


Lambda     K      H
   0.319    0.135    0.404 

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: 608
Number of extensions: 17
Number of successful extensions: 4
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: 455
Length of database: 464
Length adjustment: 33
Effective length of query: 422
Effective length of database: 431
Effective search space:   181882
Effective search space used:   181882
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: 51 (24.3 bits)

Align candidate WP_058929394.1 AU252_RS02595 (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.27605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-207  673.9   0.0   5.2e-207  673.6   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058929394.1  AU252_RS02595 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058929394.1  AU252_RS02595 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.6   0.0  5.2e-207  5.2e-207       4     439 ..      28     461 ..      26     464 .] 0.99

  Alignments for each domain:
  == domain 1  score: 673.6 bits;  conditional E-value: 5.2e-207
                                 TIGR01358   4 eswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 
                                               + wr+ p  q+P + d++  +a l +l+ lPPlv+age++ l+e+la++a+G+afllqgGdcae+f++ 
  lcl|NCBI__GCF_001484605.1:WP_058929394.1  28 DDWRDLPVSQQPSWQDKDVFDASLGELSVLPPLVFAGEVDVLRERLAAAAEGKAFLLQGGDCAETFEAA 96 
                                               78******************************************************************* PP

                                 TIGR01358  73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdea 141
                                               +ad+i+ +++++lqmavvltyga +Pv+k+gr+aGq+akPrs++ e++dgvtlp+yrGd++ng +f+ +
  lcl|NCBI__GCF_001484605.1:WP_058929394.1  97 TADKISARVKTILQMAVVLTYGAAMPVIKMGRMAGQFAKPRSSNDETRDGVTLPAYRGDIVNGYEFTPE 165
                                               ********************************************************************* PP

                                 TIGR01358 142 arvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfms 210
                                               +r +d+ r+++ay++sa+tlnl+ra+t+gG+adl+ vh+Wn+ f++  pa arye la++id+a++fm 
  lcl|NCBI__GCF_001484605.1:WP_058929394.1 166 SRGHDAARMLKAYHTSASTLNLIRAFTQGGFADLRSVHQWNKGFTE-NPAHARYESLARDIDRAIKFMA 233
                                               ********************************************86.6999****************** PP

                                 TIGR01358 211 avgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvk 279
                                               ++g + +  lkrve+++sheallldye+altr ds++g  +d+sah+lWiGertr+ld+ahv+fl++v+
  lcl|NCBI__GCF_001484605.1:WP_058929394.1 234 SCGADFEA-LKRVEFFASHEALLLDYERALTRIDSRTGFPYDTSAHFLWIGERTRELDHAHVDFLSRVR 301
                                               ***98877.************************************************************ PP

                                 TIGR01358 280 nPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmh 348
                                               nPig+k+gps+++d++l+li++ldPe+ePGrlt+i+r+Ga +i+eklP ++e+v+a+G++v+Wvtdpmh
  lcl|NCBI__GCF_001484605.1:WP_058929394.1 302 NPIGVKLGPSTTGDDALRLIDKLDPEREPGRLTFITRMGAGNIREKLPAIVEKVTASGAKVLWVTDPMH 370
                                               ********************************************************************* PP

                                 TIGR01358 349 GntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryet 417
                                               Gnt+++++Gyktr+fdd+++ev++ffevh+a+Gt pGG+h+e+tG+dv+eclGGa+ + ++ + ++ye+
  lcl|NCBI__GCF_001484605.1:WP_058929394.1 371 GNTVTSPNGYKTRNFDDVIDEVRGFFEVHHALGTVPGGLHVEMTGDDVAECLGGADPVDQEAFLDKYES 439
                                               ********************************************************************* PP

                                 TIGR01358 418 acdPrlnaeqslelaflvaekl 439
                                                cdPrln+ qsle+aflva  l
  lcl|NCBI__GCF_001484605.1:WP_058929394.1 440 VCDPRLNHMQSLEMAFLVAGAL 461
                                               ******************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (464 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: 7.60
//
[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