Alignments for a candidate for aroG in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Rhodobacter sphaeroides ATCC 17029

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011841103.1 RSPH17029_RS07920 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000015985.1:WP_011841103.1
          Length = 456

 Score =  542 bits (1397), Expect = e-159
 Identities = 272/453 (60%), Positives = 340/453 (75%), Gaps = 4/453 (0%)

Query: 75  WTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFLL 134
           WT   W+ K  +Q+PDYP+A  +++V   +  +PP+VFAGEAR L+  LA+AA G+AFLL
Sbjct: 5   WTKTDWRAKPRIQMPDYPDAAAVKAVEGQLAKYPPLVFAGEARKLKAALAEAAEGRAFLL 64

Query: 135 QGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEEK 194
           QGGDCAESF EF+A NIRDTFRVLLQM+IVLT+G +VPV+KVGRMAGQFAKPRS   E  
Sbjct: 65  QGGDCAESFSEFSADNIRDTFRVLLQMAIVLTYGAKVPVVKVGRMAGQFAKPRSAPTEVI 124

Query: 195 DGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVTQ 254
           +G++LPSY+GD ING     ++RIPDP RM++AYTQ+AA+LNLLRAF+TGG+A I RV  
Sbjct: 125 NGMELPSYRGDIINGFDPSPEARIPDPQRMLQAYTQAAASLNLLRAFSTGGFADIHRVHS 184

Query: 255 WNLDFVEQSEQADRYQELANRVDEALGFMSACGLG--TDHPLMTTTDFYTSHECLLLPYE 312
           W L F EQ ++A+RY++++NR+ +AL FMSA G+   T H L +T DFYTSHE LLL YE
Sbjct: 185 WTLGFCEQ-DKAERYRDISNRISDALDFMSAAGVNGSTSHNL-STVDFYTSHEALLLEYE 242

Query: 313 QSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVK 372
           ++L R+DS +G     S HM+W G+RTRQ+DGAHVEF RG+ NP+G+K        +L  
Sbjct: 243 EALCRIDSITGQPVAGSGHMIWIGDRTRQIDGAHVEFCRGVLNPIGLKCGPSTTVEDLKV 302

Query: 373 LVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCG 432
           L+  LNP N+ GR+T+I R GA  +   LP LIRAVR  G  VTW CDPMHGNTIKA  G
Sbjct: 303 LMARLNPQNEAGRLTLIARFGAGKVGEHLPRLIRAVREEGAKVTWCCDPMHGNTIKAASG 362

Query: 433 LKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHT 492
            KTR FDS+L EVR F  +H+ EGS  GG+H EMTGQ+VTEC GG R VT +DLS+RYHT
Sbjct: 363 YKTRPFDSVLREVREFFSIHKAEGSIPGGVHFEMTGQDVTECTGGLRAVTDEDLSNRYHT 422

Query: 493 HCDPRLNASQSLELAFIVAERLRKRRTGSQRVS 525
            CDPRLNASQSLELAF+VAE L   R  ++RV+
Sbjct: 423 ACDPRLNASQSLELAFLVAEELTTMREAARRVA 455


Lambda     K      H
   0.318    0.132    0.389 

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: 665
Number of extensions: 15
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: 525
Length of database: 456
Length adjustment: 34
Effective length of query: 491
Effective length of database: 422
Effective search space:   207202
Effective search space used:   207202
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: 52 (24.6 bits)

Align candidate WP_011841103.1 RSPH17029_RS07920 (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.2429.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-214  697.9   0.0   2.5e-214  697.7   0.0    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011841103.1  RSPH17029_RS07920 3-deoxy-7-phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011841103.1  RSPH17029_RS07920 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.7   0.0  2.5e-214  2.5e-214       1     441 [.       5     446 ..       5     448 .. 0.98

  Alignments for each domain:
  == domain 1  score: 697.7 bits;  conditional E-value: 2.5e-214
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               w++  wr+kp  q+P+yPda+a++av+ +l+++PPlv+age++klk+ lae+a+G+afllqgGdcaesf
  lcl|NCBI__GCF_000015985.1:WP_011841103.1   5 WTKTDWRAKPRIQMPDYPDAAAVKAVEGQLAKYPPLVFAGEARKLKAALAEAAEGRAFLLQGGDCAESF 73 
                                               78899**************************************************************** PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                               +e++adnird++rvllqma+vltyga++Pvvkvgr+aGq+akPrs+p+e+ +g++lpsyrGd+ing+++
  lcl|NCBI__GCF_000015985.1:WP_011841103.1  74 SEFSADNIRDTFRVLLQMAIVLTYGAKVPVVKVGRMAGQFAKPRSAPTEVINGMELPSYRGDIINGFDP 142
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               + +ar+pdp+r+++ay+++aa+lnllra+ +gG+ad+++vh+W+l f ++ ++++ry++++++i++al 
  lcl|NCBI__GCF_000015985.1:WP_011841103.1 143 SPEARIPDPQRMLQAYTQAAASLNLLRAFSTGGFADIHRVHSWTLGFCEQ-DKAERYRDISNRISDALD 210
                                               ***********************************************987.6799************** PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fmsa+gv+ ++  +l++v++ytshealll+yeeal r ds +gq    s+h++WiG+rtrq+dgahvef
  lcl|NCBI__GCF_000015985.1:WP_011841103.1 211 FMSAAGVNGSTshNLSTVDFYTSHEALLLEYEEALCRIDSITGQPVAGSGHMIWIGDRTRQIDGAHVEF 279
                                               ******98766569******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                                rgv nPig+k+gps+++++l  l+ +l+P+ne Grltli+r+Ga k+ e+lP+l++av+++G++v+W 
  lcl|NCBI__GCF_000015985.1:WP_011841103.1 280 CRGVLNPIGLKCGPSTTVEDLKVLMARLNPQNEAGRLTLIARFGAGKVGEHLPRLIRAVREEGAKVTWC 348
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGnt++aasGyktr fd++l ev+eff +hkaeG+ pGGvh e+tG+dvtec+GG r++t++dl+
  lcl|NCBI__GCF_000015985.1:WP_011841103.1 349 CDPMHGNTIKAASGYKTRPFDSVLREVREFFSIHKAEGSIPGGVHFEMTGQDVTECTGGLRAVTDEDLS 417
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441
                                               +ry+tacdPrlna+qslelaflvae l  
  lcl|NCBI__GCF_000015985.1:WP_011841103.1 418 NRYHTACDPRLNASQSLELAFLVAEELTT 446
                                               *************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (456 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: 11.35
//
[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