Alignments for a candidate for aroG in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Methylocapsa acidiphila B2

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_051335597.1 METAC_RS0114615 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_000427445.1:WP_051335597.1
          Length = 364

 Score =  454 bits (1169), Expect = e-132
 Identities = 228/344 (66%), Positives = 263/344 (76%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DDLRI EIKEL  P  ++ + P TE A  TV +AR A+ +IL+G DDRL VVIGPCSIHD
Sbjct: 17  DDLRICEIKELATPAEIIRECPRTETATKTVINARDALRRILRGEDDRLAVVIGPCSIHD 76

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
           PVAA++YA RL   R+ L  ELEI MRVYFEKPRTTVGWKGLINDPH+D SF I+ GLRI
Sbjct: 77  PVAARDYAARLAEARKRLAGELEIFMRVYFEKPRTTVGWKGLINDPHLDGSFAIDQGLRI 136

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR LLLD+ND GLPA  EFLDMITPQY+ADL+SWGAIGARTTESQVHRELASGLSCP+GF
Sbjct: 137 ARGLLLDVNDLGLPAGCEFLDMITPQYIADLVSWGAIGARTTESQVHRELASGLSCPIGF 196

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGTDG +++A+DA+ AA  PH FL+VTK G SAI +T+GN DCHIILRGG  PNY A  
Sbjct: 197 KNGTDGNVRIAVDAVKAASCPHHFLAVTKTGQSAIASTAGNEDCHIILRGGNAPNYDAAS 256

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           VA       K+G+   +MID SHANS K+ + Q  V  DV  QIA GE+ IIGVM+ESHL
Sbjct: 257 VASACAEAVKSGVTPLLMIDASHANSRKKPENQGQVIEDVAAQIAAGEQRIIGVMIESHL 316

Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
             G Q L  G+PL YG+SITD CI WE + ALL +LA AV ARR
Sbjct: 317 RAGRQDLVPGQPLVYGQSITDGCIDWESSVALLERLAQAVAARR 360


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: 445
Number of extensions: 11
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: 364
Length adjustment: 29
Effective length of query: 321
Effective length of database: 335
Effective search space:   107535
Effective search space used:   107535
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_051335597.1 METAC_RS0114615 (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.6121.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-165  533.8   0.0   7.7e-165  533.7   0.0    1.0  1  lcl|NCBI__GCF_000427445.1:WP_051335597.1  METAC_RS0114615 3-deoxy-7-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000427445.1:WP_051335597.1  METAC_RS0114615 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.7   0.0  7.7e-165  7.7e-165       1     342 []      17     360 ..      17     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 533.7 bits;  conditional E-value: 7.7e-165
                                 TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 
                                               ddlri +i+el+tP+e++++ p te+a+++v+++r+++ +il+G+ddrl vviGPcsihdp aa +ya 
  lcl|NCBI__GCF_000427445.1:WP_051335597.1  17 DDLRICEIKELATPAEIIRECPRTETATKTVINARDALRRILRGEDDRLAVVIGPCSIHDPVAARDYAA 85 
                                               799****************************************************************** PP

                                 TIGR00034  70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                               rl++ +++l  +lei mrvyfekPrttvGWkGlindP+l++sf +++Glriar llld+++lglp+++e
  lcl|NCBI__GCF_000427445.1:WP_051335597.1  86 RLAEARKRLAGELEIFMRVYFEKPRTTVGWKGLINDPHLDGSFAIDQGLRIARGLLLDVNDLGLPAGCE 154
                                               ********************************************************************* PP

                                 TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207
                                               +ld+i+pqy+adl+swgaiGarttesqvhrelasgls+p+gfkngtdG++++a+da++aa+ +h+fl+v
  lcl|NCBI__GCF_000427445.1:WP_051335597.1 155 FLDMITPQYIADLVSWGAIGARTTESQVHRELASGLSCPIGFKNGTDGNVRIAVDAVKAASCPHHFLAV 223
                                               ********************************************************************* PP

                                 TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                               tk+Gq+ai +t+Gned+hiilrGG++pnyda++va++++e  k g ++ lmid+sh+ns+k+ ++q +v
  lcl|NCBI__GCF_000427445.1:WP_051335597.1 224 TKTGQSAIASTAGNEDCHIILRGGNAPNYDAASVASACAEAVKSGVTPLLMIDASHANSRKKPENQGQV 292
                                               ********************************************************************* PP

                                 TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342
                                                e+v++qia Ge+ iiGvmies+l+ G+q+l  +++l+yG+s+td ci+we++ all++la+av +rr
  lcl|NCBI__GCF_000427445.1:WP_051335597.1 293 IEDVAAQIAAGEQRIIGVMIESHLRAGRQDLvpGQPLVYGQSITDGCIDWESSVALLERLAQAVAARR 360
                                               ******************************9999******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (364 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: 8.18
//
[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