Alignments for a candidate for aroG in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Shewanella oneidensis MR-1

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 199942 SO0756 phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (NCBI ptt file)

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__MR1:199942
          Length = 352

 Score =  530 bits (1365), Expect = e-155
 Identities = 258/349 (73%), Positives = 298/349 (85%)

Query: 1   MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60
           M YQNDD+RI E+KELLPP+A+LE+FPA+ENAA TV +AR++IH IL   DDRLLVVIGP
Sbjct: 1   MYYQNDDVRINEVKELLPPIAILERFPASENAAATVFNARQSIHNILAREDDRLLVVIGP 60

Query: 61  CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120
           CSIHDP AA EY  RL+ LRE  +D+LEIVMRVYFEKPRTTVGWKGLINDP+MDNSF++N
Sbjct: 61  CSIHDPKAALEYGQRLVVLRERYQDQLEIVMRVYFEKPRTTVGWKGLINDPYMDNSFKLN 120

Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180
           DGLR ARKLL+D+NDSG+P AGEFLDMITPQY+AD+M WGAIGARTTESQVHRELASGLS
Sbjct: 121 DGLRTARKLLVDLNDSGMPTAGEFLDMITPQYVADMMCWGAIGARTTESQVHRELASGLS 180

Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240
           CPVGFKNGTDGTIKVAIDAI AA APH FLSVTK+GHSAIV+T GN DCHIILRGG+EPN
Sbjct: 181 CPVGFKNGTDGTIKVAIDAIGAANAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGGREPN 240

Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300
           YSA HVA++ + L KA L   +MIDFSHANSSKQ+++QM V  +V +Q+A G +AI GVM
Sbjct: 241 YSASHVAQISDQLKKAKLVDNIMIDFSHANSSKQYQRQMVVANEVAEQVAAGNQAIFGVM 300

Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           VESHLVEG Q L  G+ L YG+S+TDACIGWED++ LL  L  +V  RR
Sbjct: 301 VESHLVEGRQDLIEGQALCYGQSVTDACIGWEDSERLLAVLNQSVVERR 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: 466
Number of extensions: 4
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: 352
Length adjustment: 29
Effective length of query: 321
Effective length of database: 323
Effective search space:   103683
Effective search space used:   103683
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 199942 SO0756 (phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (NCBI ptt file))
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.12113.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-174  566.1   0.0   1.2e-174  565.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:199942  SO0756 phospho-2-dehydro-3-deoxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199942  SO0756 phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.9   0.0  1.2e-174  1.2e-174       1     342 []       6     349 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 565.9 bits;  conditional E-value: 1.2e-174
                       TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklk 79 
                                     dd+ri +++ell+P ++ ++fp++e+aa++v ++r++i++ila +ddrllvviGPcsihdp+aaley +rl  l+e+++
  lcl|FitnessBrowser__MR1:199942   6 DDVRINEVKELLPPIAILERFPASENAAATVFNARQSIHNILAREDDRLLVVIGPCSIHDPKAALEYGQRLVVLRERYQ 84 
                                     799**************************************************************************** PP

                       TIGR00034  80 ddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgaiG 158
                                     d+leivmrvyfekPrttvGWkGlindP++++sf++n+Glr arkll+dl++ g+p+a+e+ld+i+pqy+ad+++wgaiG
  lcl|FitnessBrowser__MR1:199942  85 DQLEIVMRVYFEKPRTTVGWKGLINDPYMDNSFKLNDGLRTARKLLVDLNDSGMPTAGEFLDMITPQYVADMMCWGAIG 163
                                     ******************************************************************************* PP

                       TIGR00034 159 arttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnyd 237
                                     arttesqvhrelasgls+pvgfkngtdG++kvaidai aa+a+h+flsvtk G++aiv+tkGn+d+hiilrGG++pny+
  lcl|FitnessBrowser__MR1:199942 164 ARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAIGAANAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGGREPNYS 242
                                     ******************************************************************************* PP

                       TIGR00034 238 aedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyG 314
                                     a++va++ ++l+ka+l +++midfsh+ns+k+y+rq+ va++v+eq+a G++ai+Gvm+es+l+eG+q+l  +++l yG
  lcl|FitnessBrowser__MR1:199942 243 ASHVAQISDQLKKAKLVDNIMIDFSHANSSKQYQRQMVVANEVAEQVAAGNQAIFGVMVESHLVEGRQDLieGQALCYG 321
                                     *********************************************************************988899**** PP

                       TIGR00034 315 ksvtdacigwedteallrklaeavkerr 342
                                     +svtdacigwed+e+ll+ l+++v err
  lcl|FitnessBrowser__MR1:199942 322 QSVTDACIGWEDSERLLAVLNQSVVERR 349
                                     ***********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (352 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: 00:00:00.01
# Mc/sec: 9.41
//
[ok]

This GapMind analysis is from Apr 09 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