Alignments for a candidate for aroG in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Thiohalomonas denitrificans HLD2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_092991507.1 BLP65_RS00420 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::Q9WYH8
         (338 letters)



>NCBI__GCF_900102855.1:WP_092991507.1
          Length = 338

 Score =  332 bits (851), Expect = 8e-96
 Identities = 168/335 (50%), Positives = 230/335 (68%), Gaps = 1/335 (0%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60
           MI+++  G +EE I  V K  ES  L  ++S+G ERTVIG IGD+     +  ++L  VE
Sbjct: 1   MIIIMSTGVSEEHIAGVEKRLESMGLGSNVSRGIERTVIGAIGDETKADKEALQALPGVE 60

Query: 61  SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSEL 120
            V+RV+KPYK+V+R +H EDTV+D+G VK+G     +IAGPCSVE +E +   A  +   
Sbjct: 61  DVIRVMKPYKIVARSYHKEDTVVDIGGVKLGGNTVQVIAGPCSVETQEQMDRAAEMVVAA 120

Query: 121 GVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEY-AD 179
           G +++RGGA+KPRTSPYSFQG G +GLE  R AADK  + +VTE +    L    EY  D
Sbjct: 121 GCRLMRGGAFKPRTSPYSFQGHGVEGLEIFRAAADKQKLPIVTELMDVRSLDAFDEYNVD 180

Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239
            IQIG RN QNF LL + G   KPV+LKRG   TI+E+L+SAEYIA  GN  II CERGI
Sbjct: 181 AIQIGTRNMQNFDLLKEVGRIQKPVILKRGMSATIKEWLMSAEYIAAGGNHNIIFCERGI 240

Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299
           RTFE   RN LD++A+P+++KE+HLP++VDPSH+GG+  +V  L+RAA+A GA G++VE+
Sbjct: 241 RTFETYYRNVLDVTAIPVLKKETHLPVIVDPSHAGGKAWMVPALARAAVAAGADGLLVEM 300

Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334
           HP P +A  D  Q++  +    L+ E++ +A A+G
Sbjct: 301 HPSPCEAWCDADQAITPDELNALMGELRGIAKAIG 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: 316
Number of extensions: 7
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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_092991507.1 BLP65_RS00420 (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.7767.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-117  376.1   0.0   5.2e-117  375.8   0.0    1.1  1  lcl|NCBI__GCF_900102855.1:WP_092991507.1  BLP65_RS00420 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092991507.1  BLP65_RS00420 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.8   0.0  5.2e-117  5.2e-117       3     258 ..      72     328 ..      70     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 375.8 bits;  conditional E-value: 5.2e-117
                                 TIGR01361   3 askkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfq 71 
                                               ++++++ke+tvvd+ +vk+G++++ viaGPCsve +eq+ ++a++v +aG +l+rGgafkPrtsPysfq
  lcl|NCBI__GCF_900102855.1:WP_092991507.1  72 VARSYHKEDTVVDIGGVKLGGNTVQVIAGPCSVETQEQMDRAAEMVVAAGCRLMRGGAFKPRTSPYSFQ 140
                                               67899**************************************************************** PP

                                 TIGR01361  72 Glgeeglkllkrakdetgllvvtevlderdveivaey.vDilqiGarnmqnfelLkevgkskkPvlLkr 139
                                               G+g egl++ ++a+d++ l++vte++d+r ++ ++ey vD +qiG+rnmqnf+lLkevg+ +kPv+Lkr
  lcl|NCBI__GCF_900102855.1:WP_092991507.1 141 GHGVEGLEIFRAAADKQKLPIVTELMDVRSLDAFDEYnVDAIQIGTRNMQNFDLLKEVGRIQKPVILKR 209
                                               ************************************978****************************** PP

                                 TIGR01361 140 glaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrr 208
                                               g++ati+ewl++aeYi++ gn+n+i+cerGirtfe++ r+ ld++a+++lkk+thlPvivDpsha G+ 
  lcl|NCBI__GCF_900102855.1:WP_092991507.1 210 GMSATIKEWLMSAEYIAAGGNHNIIFCERGIRTFETYYRNVLDVTAIPVLKKETHLPVIVDPSHAGGKA 278
                                               ********************************************************************* PP

                                 TIGR01361 209 dlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258
                                                +v++la+aava+Gadgll+e+hp P +a++D++q +tp+e+++l+ el+
  lcl|NCBI__GCF_900102855.1:WP_092991507.1 279 WMVPALARAAVAAGADGLLVEMHPSPCEAWCDADQAITPDELNALMGELR 328
                                               **********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (338 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.51
//
[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