Alignments for a candidate for aroG in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Methylovulum miyakonense HT12

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_019864486.1 METMI_RS0101835 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_000384075.1:WP_019864486.1
          Length = 362

 Score =  458 bits (1178), Expect = e-133
 Identities = 231/348 (66%), Positives = 275/348 (79%), Gaps = 1/348 (0%)

Query: 3   YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62
           Y  DDLRI EIKE++ P+ + E+ P T+ AA T   ARK IH IL G DDR+LVVIGPCS
Sbjct: 5   YNTDDLRICEIKEVIAPILVHEELPITDAAAETTLAARKEIHNILTGADDRVLVVIGPCS 64

Query: 63  IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122
           IHDPVAAKEYA RL A+++ELKD L IVMRVYFEKPRTTVGWKGLINDP +D+SF IN G
Sbjct: 65  IHDPVAAKEYAQRLKAVKDELKDYLLIVMRVYFEKPRTTVGWKGLINDPDLDSSFNINKG 124

Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182
           LRIAR+LL+D+   G+PAA E+LD+I+PQY++DL++WGAIGARTTESQ HRELASG+SCP
Sbjct: 125 LRIARQLLVDVTSMGMPAATEYLDLISPQYISDLIAWGAIGARTTESQGHRELASGVSCP 184

Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-PNY 241
           +GFKN TDGTIK+AIDAI AA +PH FLS+TK GHSAI +T+GN D HIILRGG + PNY
Sbjct: 185 IGFKNSTDGTIKIAIDAIGAAMSPHHFLSLTKTGHSAIFSTTGNEDVHIILRGGNDRPNY 244

Query: 242 SAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMV 301
            A  V +V EGL KA L   +MIDFSHANS KQ ++Q+ V  DV  QIA G+  I+GVMV
Sbjct: 245 DAVSVEQVAEGLRKANLRPNIMIDFSHANSLKQCQRQLIVGEDVSAQIAHGDHRIMGVMV 304

Query: 302 ESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           ESHL  G+Q    G+ L YG+SITD C+GWEDT  LL +LA AV+ RR
Sbjct: 305 ESHLKAGSQKQIEGQELVYGQSITDGCLGWEDTVPLLHELAEAVRKRR 352


Lambda     K      H
   0.317    0.134    0.397 

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: 437
Number of extensions: 10
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: 350
Length of database: 362
Length adjustment: 29
Effective length of query: 321
Effective length of database: 333
Effective search space:   106893
Effective search space used:   106893
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_019864486.1 METMI_RS0101835 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.27501.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-163  529.6   0.1   1.5e-163  529.4   0.1    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019864486.1  METMI_RS0101835 3-deoxy-7-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019864486.1  METMI_RS0101835 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.4   0.1  1.5e-163  1.5e-163       1     342 []       8     352 ..       8     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 529.4 bits;  conditional E-value: 1.5e-163
                                 TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 
                                               ddlri +i+e+++P  ++++ p+t +aae+   +rkei++il+G ddr+lvviGPcsihdp aa+eya+
  lcl|NCBI__GCF_000384075.1:WP_019864486.1   8 DDLRICEIKEVIAPILVHEELPITDAAAETTLAARKEIHNILTGADDRVLVVIGPCSIHDPVAAKEYAQ 76 
                                               799****************************************************************** PP

                                 TIGR00034  70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                               rlk+++++lkd l ivmrvyfekPrttvGWkGlindPdl+ sf++nkGlriar+ll+d++ +g+p+ate
  lcl|NCBI__GCF_000384075.1:WP_019864486.1  77 RLKAVKDELKDYLLIVMRVYFEKPRTTVGWKGLINDPDLDSSFNINKGLRIARQLLVDVTSMGMPAATE 145
                                               ********************************************************************* PP

                                 TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207
                                               +ld ispqy++dl++wgaiGarttesq hrelasg+s+p+gfkn+tdG++k+aidai aa ++h+fls 
  lcl|NCBI__GCF_000384075.1:WP_019864486.1 146 YLDLISPQYISDLIAWGAIGARTTESQGHRELASGVSCPIGFKNSTDGTIKIAIDAIGAAMSPHHFLSL 214
                                               ********************************************************************* PP

                                 TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275
                                               tk+G++ai +t+Gned hiilrGG++ pnyda +v++v e l+ka+l++++midfsh+ns k+ +rql 
  lcl|NCBI__GCF_000384075.1:WP_019864486.1 215 TKTGHSAIFSTTGNEDVHIILRGGNDrPNYDAVSVEQVAEGLRKANLRPNIMIDFSHANSLKQCQRQLI 283
                                               *************************99****************************************** PP

                                 TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342
                                               v e+v++qia+G++ i+Gvm+es+l+ G+q+   ++el+yG+s+td c+gwedt  ll++laeav++rr
  lcl|NCBI__GCF_000384075.1:WP_019864486.1 284 VGEDVSAQIAHGDHRIMGVMVESHLKAGSQKQieGQELVYGQSITDGCLGWEDTVPLLHELAEAVRKRR 352
                                               *****************************9876899******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (362 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.95
//
[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