Alignments for a candidate for aroB in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Hydrogenophaga taeniospiralis NBRC 102512

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_068174426.1 HTA01S_RS19525 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_001592305.1:WP_068174426.1
          Length = 373

 Score =  373 bits (957), Expect = e-108
 Identities = 198/351 (56%), Positives = 241/351 (68%), Gaps = 3/351 (0%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAG 61
           E++ + LG+RSY I I  GL +  +S+  L +    ++VTNET+APLYL +++  L    
Sbjct: 11  EQVQIHLGDRSYSIVIGPGLLDASSSYAGLPTAASAVIVTNETVAPLYLLRLQTALASHF 70

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
             +  V LPDGE +K+   L+ +F ALL+    R T L ALGGGVVGD+TGFAAASY RG
Sbjct: 71  DTIHVVTLPDGEAFKTWESLNLIFDALLRHGCDRKTVLFALGGGVVGDMTGFAAASYMRG 130

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
           V F+QVPTTLL+QVDSSVGGKTA+NHPLGKNMIGAFYQP  V+ DLD L TLPPREL++G
Sbjct: 131 VPFVQVPTTLLAQVDSSVGGKTAINHPLGKNMIGAFYQPQRVICDLDTLNTLPPRELSAG 190

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
           LAEVIKYG I D AF  W+E ++  LL  D   MAY +RR CE+KA VV  DERE+GLRA
Sbjct: 191 LAEVIKYGPIADMAFLEWMEAHVAELLARDPATMAYAVRRSCEIKAHVVGQDERESGLRA 250

Query: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301
           +LN GHTFGHAIEA MGYG WLHGEAV  GMVMAAR S+RLG        R+  L++R G
Sbjct: 251 ILNFGHTFGHAIEAGMGYGRWLHGEAVGCGMVMAARLSQRLGLVEDGFVVRLTRLIERVG 310

Query: 302 LPVNGP---REMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSH 349
           LPV  P      +A  YL  M  DKK  AGE++ +L    G + VR    H
Sbjct: 311 LPVVAPVLDGADNAGRYLALMRVDKKSEAGEIKFVLIDGSGNALVRGAPDH 361


Lambda     K      H
   0.320    0.136    0.392 

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: 348
Number of extensions: 11
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: 362
Length of database: 373
Length adjustment: 30
Effective length of query: 332
Effective length of database: 343
Effective search space:   113876
Effective search space used:   113876
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: 49 (23.5 bits)

Align candidate WP_068174426.1 HTA01S_RS19525 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.26300.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-119  384.0   0.0     4e-119  383.8   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068174426.1  HTA01S_RS19525 3-dehydroquinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068174426.1  HTA01S_RS19525 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.8   0.0    4e-119    4e-119       1     333 [.      22     357 ..      22     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 383.8 bits;  conditional E-value: 4e-119
                                 TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 
                                               y++++g gll++ +++    +a ++v++t+e+v+ l+  +l+ al+s   +++v+++pdge  K++e++
  lcl|NCBI__GCF_001592305.1:WP_068174426.1  22 YSIVIGPGLLDASSSYAGLpTAASAVIVTNETVAPLYLLRLQTALASHFDTIHVVTLPDGEAFKTWESL 90 
                                               689999****97777766567799***********************99999***************** PP

                                 TIGR01357  69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137
                                               + + d+ll+++++rk+vl a+GGGvvgD++GF+Aa+y+RG+++vqvPTtlla+vDssvGGKt+in+plg
  lcl|NCBI__GCF_001592305.1:WP_068174426.1  91 NLIFDALLRHGCDRKTVLFALGGGVVGDMTGFAAASYMRGVPFVQVPTTLLAQVDSSVGGKTAINHPLG 159
                                               ********************************************************************* PP

                                 TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206
                                               kN+iGafyqP+ V++dl++l+tlp rel++G+aEviK+g iad +++e++e + ++ll + + ++++ +
  lcl|NCBI__GCF_001592305.1:WP_068174426.1 160 KNMIGAFYQPQRVICDLDTLNTLPPRELSAGLAEVIKYGPIADMAFLEWMEAHVAELLAR-DPATMAYA 227
                                               *******************************************************99976.5599**** PP

                                 TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274
                                               ++rs+e+Ka+vV +De+esglRa+LNfGHt+gHaiEa ++y+ + HGeaV +Gmv++a+ls++lgl++ 
  lcl|NCBI__GCF_001592305.1:WP_068174426.1 228 VRRSCEIKAHVVGQDERESGLRAILNFGHTFGHAIEAGMGYGrWLHGEAVGCGMVMAARLSQRLGLVED 296
                                               ********************************************************************* PP

                                 TIGR01357 275 ellerlvallkklglptklkk...klsveellkallkDKKnegskiklvlleeiGkaalase 333
                                                 + rl++l++++glp+  +      ++  +l+ +  DKK+e+++ik+vl++  G+a ++  
  lcl|NCBI__GCF_001592305.1:WP_068174426.1 297 GFVVRLTRLIERVGLPVVAPVldgADNAGRYLALMRVDKKSEAGEIKFVLIDGSGNALVR-G 357
                                               *****************9998777888999*************************99877.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (373 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.07
//
[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