Alignments for a candidate for aroG in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Methylobacterium nodulans ORS 2060

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_015927953.1 MNOD_RS06070 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::P29976
         (525 letters)



>NCBI__GCF_000022085.1:WP_015927953.1
          Length = 460

 Score =  534 bits (1376), Expect = e-156
 Identities = 257/444 (57%), Positives = 332/444 (74%), Gaps = 2/444 (0%)

Query: 74  KWTPESWKLKKALQLPDYPNANELESVLKTIEAFPPIVFAGEARNLEERLADAAVGKAFL 133
           +WTP SW+     Q+P+YP+A  LE+V + +E+FPP+VFAGEAR L++ LA  A G+AFL
Sbjct: 4   RWTPSSWRRLPIQQVPEYPDAVALEAVERQLESFPPLVFAGEARKLKKSLAKVAAGEAFL 63

Query: 134 LQGGDCAESFKEFNATNIRDTFRVLLQMSIVLTFGGQVPVIKVGRMAGQFAKPRSDAFEE 193
           LQGGDCAESF E +A NIRD FRV LQM++VLTF G  PV+KVGR+AGQFAKPRS   E 
Sbjct: 64  LQGGDCAESFDEHSADNIRDFFRVFLQMALVLTFAGGSPVVKVGRIAGQFAKPRSSPTET 123

Query: 194 KDGVKLPSYKGDNINGDTFDEKSRIPDPNRMIRAYTQSAATLNLLRAFATGGYAAIQRVT 253
            +GV LPSY+GD +NG  F  + RIPDP R + AY QSAATLNLLRAFA+GGYA ++   
Sbjct: 124 VNGVALPSYRGDIVNGIGFSAEDRIPDPKRQLEAYRQSAATLNLLRAFASGGYANLENAH 183

Query: 254 QWNLDFVEQSEQADRYQELANRVDEALGFMSACGLGTD-HPLMTTTDFYTSHECLLLPYE 312
           +W L FV+ S Q+  Y++LA R+ E L FM A G+  + H  +  TDFYTSHE LLL YE
Sbjct: 184 RWMLGFVKDSPQSSAYEDLAQRMTETLDFMRAIGINPETHQEVRQTDFYTSHEALLLGYE 243

Query: 313 QSLTRLDSTSGLYYDCSAHMVWCGERTRQLDGAHVEFLRGIANPLGIKVSNKMDPFELVK 372
           Q+LTR+DSTSG +Y  S HM+W G+RTRQ D AH+E+ RGI NP+G+K    + P +L++
Sbjct: 244 QALTRVDSTSGDWYATSGHMLWIGDRTRQADHAHIEYARGIRNPIGLKCGPSLQPDDLIR 303

Query: 373 LVEILNPNNKPGRITVIVRMGAENMRVKLPHLIRAVRRSGQIVTWVCDPMHGNTIKAPCG 432
           L+ +LNP N+PGR+T+I R GA+ +   LP LIRAV R G+ V W CDPMHGNTI A  G
Sbjct: 304 LIGLLNPENEPGRLTLICRFGADKVGDHLPGLIRAVEREGRKVVWSCDPMHGNTITA-SG 362

Query: 433 LKTRAFDSILAEVRAFLDVHEQEGSHAGGIHLEMTGQNVTECIGGSRTVTYDDLSSRYHT 492
            KTR F+ ++ E++ F DVH  EG++AGGIHLEMTG+NVTEC GG+R +T +DL  RYHT
Sbjct: 363 YKTRPFERVMKEIQGFFDVHRAEGTYAGGIHLEMTGKNVTECTGGARALTAEDLQDRYHT 422

Query: 493 HCDPRLNASQSLELAFIVAERLRK 516
           +CDPRLNA Q+LE+AF+ A+ +++
Sbjct: 423 YCDPRLNAEQALEVAFLTADLVKR 446


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: 647
Number of extensions: 25
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: 460
Length adjustment: 34
Effective length of query: 491
Effective length of database: 426
Effective search space:   209166
Effective search space used:   209166
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_015927953.1 MNOD_RS06070 (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.2721993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-215  701.9   0.0   1.6e-215  701.6   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015927953.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015927953.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  701.6   0.0  1.6e-215  1.6e-215       1     440 [.       5     445 ..       5     448 .. 0.99

  Alignments for each domain:
  == domain 1  score: 701.6 bits;  conditional E-value: 1.6e-215
                             TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkeve 73 
                                           w+++swr  p +q+PeyPda aleav+ +les+PPlv+age++klk++la+va+GeafllqgGdcaesf+e +
  NCBI__GCF_000022085.1:WP_015927953.1   5 WTPSSWRRLPIQQVPEYPDAVALEAVERQLESFPPLVFAGEARKLKKSLAKVAAGEAFLLQGGDCAESFDEHS 77 
                                           89*********************************************************************** PP

                             TIGR01358  74 adnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdeaarvpd 146
                                           adnird +rv+lqma+vlt++++ PvvkvgriaGq+akPrs+p+e+ +gv lpsyrGd++ng  f++++r+pd
  NCBI__GCF_000022085.1:WP_015927953.1  78 ADNIRDFFRVFLQMALVLTFAGGSPVVKVGRIAGQFAKPRSSPTETVNGVALPSYRGDIVNGIGFSAEDRIPD 150
                                           ************************************************************************* PP

                             TIGR01358 147 perlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfmsavgvaeae. 218
                                           p+r ++ay +saatlnllra++sgGya+l++ h+W l fvk+sp+++ ye+la++++e+l fm+a+g+++++ 
  NCBI__GCF_000022085.1:WP_015927953.1 151 PKRQLEAYRQSAATLNLLRAFASGGYANLENAHRWMLGFVKDSPQSSAYEDLAQRMTETLDFMRAIGINPETh 223
                                           ********************************************************************98877 PP

                             TIGR01358 219 .alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvknPigikvgpsm 290
                                            +++++++ytshealll ye+altrvds++g+++ +s+h+lWiG+rtrq d+ah+e++rg++nPig+k+gps+
  NCBI__GCF_000022085.1:WP_015927953.1 224 qEVRQTDFYTSHEALLLGYEQALTRVDSTSGDWYATSGHMLWIGDRTRQADHAHIEYARGIRNPIGLKCGPSL 296
                                           79*********************************************************************** PP

                             TIGR01358 291 eadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmhGntleaasGyktrrf 363
                                           ++d+l++li  l+PenePGrltli r+Ga+k+ ++lP l++av+++Gr+vvW +dpmhGnt++ asGyktr f
  NCBI__GCF_000022085.1:WP_015927953.1 297 QPDDLIRLIGLLNPENEPGRLTLICRFGADKVGDHLPGLIRAVEREGRKVVWSCDPMHGNTIT-ASGYKTRPF 368
                                           *************************************************************86.68******* PP

                             TIGR01358 364 ddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryetacdPrlnaeqslelaflva 436
                                           +++++e+++ff+vh+aeGt+ GG+hle+tG++vtec+GGar++t +dl++ry+t cdPrlnaeq+le+afl a
  NCBI__GCF_000022085.1:WP_015927953.1 369 ERVMKEIQGFFDVHRAEGTYAGGIHLEMTGKNVTECTGGARALTAEDLQDRYHTYCDPRLNAEQALEVAFLTA 441
                                           ***********************************************************************99 PP

                             TIGR01358 437 eklr 440
                                           + ++
  NCBI__GCF_000022085.1:WP_015927953.1 442 DLVK 445
                                           9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (460 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.51
//
[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