Alignments for a candidate for aroG in Brevundimonas sp. GW460-12-10-14-LB2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Brevundimonas sp. GW460-12-10-14-LB2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_066551689.1 A4249_RS06840 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::A0A0D5ZBC4
         (539 letters)



>NCBI__GCF_001636925.1:WP_066551689.1
          Length = 456

 Score =  553 bits (1426), Expect = e-162
 Identities = 271/448 (60%), Positives = 336/448 (75%), Gaps = 2/448 (0%)

Query: 82  KWTVDSWKSKKALQLP-EYPDQAELESVLKTLDAFPPIVFAGEARSLEEKLGEAAMGNAF 140
           +WT +SW++K AL +P +YPD A L  V   L A PP+VFAGEAR L  KL +   G+AF
Sbjct: 3   RWTPESWRTKTALHMPADYPDPAALARVEDELRALPPLVFAGEARRLTSKLAQVERGDAF 62

Query: 141 LLQGGDCAESFKEFNANNIRDTFRILLQMGAVLMFGGQMPVIKVGRMAGQFAKPRSDPFE 200
           LLQGGDCAESFKEF+ +NIRDTFR++LQM  VL F G+ PV+KVGR+AGQFAKPRS P E
Sbjct: 63  LLQGGDCAESFKEFSTDNIRDTFRLILQMAVVLTFAGRKPVVKVGRIAGQFAKPRSSPLE 122

Query: 201 EKNGVKLPSYRGDNVNGDSFDEKSRIPDPQRMIRAYCQSAATLNLLRAFATGGYAAMQRV 260
           E +GV+LPSYRGD +NG  F  + R PDPQR+IRAY QSA+TLNLLRAFA GGYA +  +
Sbjct: 123 EIDGVELPSYRGDIINGMGFTAEERAPDPQRLIRAYNQSASTLNLLRAFAGGGYADLYNI 182

Query: 261 TQWNLDFTEHSEQGDRYRELASRVDEALGFMAAAGLTVD-HPIMTTTEFWTSHECLLLPY 319
            +W L F   +  G +YRELA ++ EAL FM A G+T + HP ++  E +TSHE LLL  
Sbjct: 183 HRWTLGFAGDNAAGAQYRELADKITEALAFMEAVGVTPETHPDLSRVEVFTSHEALLLNV 242

Query: 320 EQSLTRLDSTSGRYYDCSAHFLWAGERTRQLDGAHVEFLRGVANPLGIKVSDKMDPNELV 379
           E +LTRLD  SG ++D SAH LW GERTRQLDGAHVEF++G+ NP+G+K    M  ++L+
Sbjct: 243 ESALTRLDGGSGEWFDTSAHMLWIGERTRQLDGAHVEFMKGIKNPIGVKCGPTMTADDLL 302

Query: 380 KLIEILNPQNKAGRITVITRMGAENMRVKLPHLIRAVRRAGQIVTWVSDPMHGNTIKAPC 439
            LI+ LNP N +GR+T+I R G + +  +LP L+R V+ +G+ V W  DPMHGNT+KA  
Sbjct: 303 PLIDALNPDNVSGRLTLIGRFGHDKVGERLPKLMREVKASGRKVIWSIDPMHGNTLKAGN 362

Query: 440 GLKTRPFDSIRAEVRAFFDVHEQEGSHPGGVHLEMTGQNVTECIGGSRTVTFDDLGSRYH 499
           G KTRPFD I  EVR F DV E EG HPGGVHLEMTGQNVTECIGG++ VT DDL +RYH
Sbjct: 363 GYKTRPFDRILGEVRTFIDVAEAEGVHPGGVHLEMTGQNVTECIGGAQAVTEDDLSNRYH 422

Query: 500 THCDPRLNASQSLELAFIIAERLRKRRI 527
           THCDPRLNA Q+LELAF++AERL+  R+
Sbjct: 423 THCDPRLNADQALELAFLVAERLKAGRV 450


Lambda     K      H
   0.318    0.133    0.393 

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: 709
Number of extensions: 24
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: 539
Length of database: 456
Length adjustment: 34
Effective length of query: 505
Effective length of database: 422
Effective search space:   213110
Effective search space used:   213110
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_066551689.1 A4249_RS06840 (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.2048518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-224  730.7   0.0   2.8e-224  730.5   0.0    1.0  1  NCBI__GCF_001636925.1:WP_066551689.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001636925.1:WP_066551689.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.5   0.0  2.8e-224  2.8e-224       1     441 [.       4     447 ..       4     449 .. 0.99

  Alignments for each domain:
  == domain 1  score: 730.5 bits;  conditional E-value: 2.8e-224
                             TIGR01358   1 wsleswrskpaaqlP.eyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 
                                           w++eswr+k+a+++P +yPd +al +v+d+l+ lPPlv+age+++l +kla+v +G+afllqgGdcaesfke+
  NCBI__GCF_001636925.1:WP_066551689.1   4 WTPESWRTKTALHMPaDYPDPAALARVEDELRALPPLVFAGEARRLTSKLAQVERGDAFLLQGGDCAESFKEF 76 
                                           89*************9********************************************************* PP

                             TIGR01358  73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvp 145
                                           ++dnird++r++lqmavvlt+++++PvvkvgriaGq+akPrs+p+e+ dgv+lpsyrGd+ing+ f++++r p
  NCBI__GCF_001636925.1:WP_066551689.1  77 STDNIRDTFRLILQMAVVLTFAGRKPVVKVGRIAGQFAKPRSSPLEEIDGVELPSYRGDIINGMGFTAEERAP 149
                                           ************************************************************************* PP

                             TIGR01358 146 dperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae 218
                                           dp+rl+ray++sa+tlnllra++ gGyadl+++h+W+l f ++  aga+y++la++i+eal fm+avgv++++
  NCBI__GCF_001636925.1:WP_066551689.1 150 DPQRLIRAYNQSASTLNLLRAFAGGGYADLYNIHRWTLGFAGDNAAGAQYRELADKITEALAFMEAVGVTPET 222
                                           **********************************************************************998 PP

                             TIGR01358 219 ..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgps 289
                                             +l+rve++tshealll+ e+altr d  +g++fd+sah+lWiGertrqldgahvef++g+knPig+k+gp+
  NCBI__GCF_001636925.1:WP_066551689.1 223 hpDLSRVEVFTSHEALLLNVESALTRLDGGSGEWFDTSAHMLWIGERTRQLDGAHVEFMKGIKNPIGVKCGPT 295
                                           899********************************************************************** PP

                             TIGR01358 290 meadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrr 362
                                           m+ad+ll li+ l+P+n  Grltli r+G +k+ e+lP+l+++vka+Gr+v+W  dpmhGntl+a++Gyktr 
  NCBI__GCF_001636925.1:WP_066551689.1 296 MTADDLLPLIDALNPDNVSGRLTLIGRFGHDKVGERLPKLMREVKASGRKVIWSIDPMHGNTLKAGNGYKTRP 368
                                           ************************************************************************* PP

                             TIGR01358 363 fddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflv 435
                                           fd+il ev++f++v++aeG+hpGGvhle+tG++vtec+GGa+++te+dl++ry+t+cdPrlna+q+lelaflv
  NCBI__GCF_001636925.1:WP_066551689.1 369 FDRILGEVRTFIDVAEAEGVHPGGVHLEMTGQNVTECIGGAQAVTEDDLSNRYHTHCDPRLNADQALELAFLV 441
                                           ************************************************************************* PP

                             TIGR01358 436 aeklre 441
                                           ae+l++
  NCBI__GCF_001636925.1:WP_066551689.1 442 AERLKA 447
                                           ***996 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.57
//
[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