Alignments for a candidate for aroG in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Mesorhizobium ciceri WSM1271

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate YP_004139720.1 Mesci_0498 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_000185905.1:YP_004139720.1
          Length = 363

 Score =  430 bits (1105), Expect = e-125
 Identities = 209/344 (60%), Positives = 260/344 (75%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DDLR+KEI+EL  P  ++ + P T  A  TV+ +R A H IL G DDRLLV++GPCSIHD
Sbjct: 6   DDLRVKEIRELSTPDEVMREIPRTLTATRTVSASRNATHAILNGTDDRLLVIVGPCSIHD 65

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
           PVAA +YA+RL ALRE L D LEIVMRVYFEKPRTTVGWKGLINDP +D SF I+ GLR+
Sbjct: 66  PVAAVDYASRLAALRESLSDRLEIVMRVYFEKPRTTVGWKGLINDPDLDGSFNIDKGLRM 125

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR +L  +N+ GLPAA EFLDM TPQY+ADL++WGAIGARTTESQ+HRELASGLSCPVGF
Sbjct: 126 ARNVLSAVNNLGLPAATEFLDMTTPQYIADLVAWGAIGARTTESQIHRELASGLSCPVGF 185

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGTDG +++A +A+ +A  PH F++VTK G S I  T+GN DCH+ILRGG +PNY    
Sbjct: 186 KNGTDGNLRIAAEAVKSAAQPHHFMAVTKGGRSGIATTTGNEDCHVILRGGVQPNYDTAS 245

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           V      L + G+  ++MID SHANS+K+ + Q  V ADV  Q+A G++ IIG+M+ES+L
Sbjct: 246 VEAAAVELARIGVAPRLMIDVSHANSAKKPENQPKVAADVAGQVAAGDERIIGLMIESNL 305

Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           V G Q +  G+PL YG+SITD CI W  T+ +L  LA AV+ RR
Sbjct: 306 VAGRQDVVPGKPLVYGQSITDGCIDWATTETVLHGLAGAVEWRR 349


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: 410
Number of extensions: 10
Number of successful extensions: 1
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: 363
Length adjustment: 29
Effective length of query: 321
Effective length of database: 334
Effective search space:   107214
Effective search space used:   107214
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 YP_004139720.1 Mesci_0498 (phospho-2-dehydro-3-deoxyheptonate aldolase)
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.27944.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-160  520.1   0.0   1.2e-160  519.9   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004139720.1  Mesci_0498 phospho-2-dehydro-3-d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004139720.1  Mesci_0498 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.9   0.0  1.2e-160  1.2e-160       1     341 [.       6     348 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 519.9 bits;  conditional E-value: 1.2e-160
                                 TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 
                                               ddlr+++i el tP+e+++++p t +a+ +v  sr++ + il+G ddrllv++GPcsihdp aa++ya+
  lcl|NCBI__GCF_000185905.1:YP_004139720.1   6 DDLRVKEIRELSTPDEVMREIPRTLTATRTVSASRNATHAILNGTDDRLLVIVGPCSIHDPVAAVDYAS 74 
                                               799****************************************************************** PP

                                 TIGR00034  70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                               rl++l+e l+d+leivmrvyfekPrttvGWkGlindPdl++sf+++kGlr+ar++l  +++lglp+ate
  lcl|NCBI__GCF_000185905.1:YP_004139720.1  75 RLAALRESLSDRLEIVMRVYFEKPRTTVGWKGLINDPDLDGSFNIDKGLRMARNVLSAVNNLGLPAATE 143
                                               ********************************************************************* PP

                                 TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207
                                               +ld+ +pqy+adl++wgaiGarttesq+hrelasgls+pvgfkngtdG+l++a +a+++aa++h+f++v
  lcl|NCBI__GCF_000185905.1:YP_004139720.1 144 FLDMTTPQYIADLVAWGAIGARTTESQIHRELASGLSCPVGFKNGTDGNLRIAAEAVKSAAQPHHFMAV 212
                                               ********************************************************************* PP

                                 TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                               tk G++ i +t+Gned+h+ilrGG +pnyd+++v+++  el ++g  ++lmid+sh+ns k+ ++q++v
  lcl|NCBI__GCF_000185905.1:YP_004139720.1 213 TKGGRSGIATTTGNEDCHVILRGGVQPNYDTASVEAAAVELARIGVAPRLMIDVSHANSAKKPENQPKV 281
                                               ********************************************************************* PP

                                 TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavker 341
                                               a++v+ q+a G++ iiG+miesnl+ G+q++  +++l+yG+s+td ci+w +te++l+ la av+ r
  lcl|NCBI__GCF_000185905.1:YP_004139720.1 282 AADVAGQVAAGDERIIGLMIESNLVAGRQDVvpGKPLVYGQSITDGCIDWATTETVLHGLAGAVEWR 348
                                               ******************************9999*****************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (363 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: 8.22
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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