Aligments for a candidate for aroG in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Aligments for a candidate for aroG in Shewanella loihica PV-4

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 5208339 Shew_0851 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::P0AB91
         (350 letters)



>lcl|FitnessBrowser__PV4:5208339 Shew_0851
           phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
          Length = 350

 Score =  536 bits (1380), Expect = e-157
 Identities = 263/349 (75%), Positives = 295/349 (84%)

Query: 1   MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60
           M YQ DD+RI +IKELLPPVA+LE+FPA+ENA+ TV +AR+ IH ILK  DDRLLV+IGP
Sbjct: 1   MYYQTDDVRINKIKELLPPVAILERFPASENASATVFNARQNIHNILKKEDDRLLVIIGP 60

Query: 61  CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120
           CSIHDP AA EY  RL  LRE+ KD+LE+VMRVYFEKPRTTVGWKGLINDP+MDNSF++N
Sbjct: 61  CSIHDPKAALEYGERLAKLREQYKDQLEVVMRVYFEKPRTTVGWKGLINDPYMDNSFKLN 120

Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180
           DGLR ARKLLLD+N+ G+P AGEFLDMITPQY+ADLM WGAIGARTTESQVHRELASGLS
Sbjct: 121 DGLRTARKLLLDLNELGVPTAGEFLDMITPQYVADLMCWGAIGARTTESQVHRELASGLS 180

Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240
           CPVGFKNGTDGTIKVAIDAI AA APH FLSVTK+GHSAIV+T GN DCHIILRGGKEPN
Sbjct: 181 CPVGFKNGTDGTIKVAIDAIGAASAPHHFLSVTKYGHSAIVSTKGNPDCHIILRGGKEPN 240

Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300
           YSA+HV  + E L KA LP  +M+DFSHANSSKQFK+QM V  DV  Q++ GE+AI GVM
Sbjct: 241 YSAEHVQAISEQLAKANLPQNIMVDFSHANSSKQFKRQMLVGEDVASQVSAGERAIFGVM 300

Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           VESHLVEG Q    G+PL YG+SITDACIGWEDT+ LL  L   V  RR
Sbjct: 301 VESHLVEGRQDYIEGQPLCYGQSITDACIGWEDTETLLANLNRCVLERR 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: 450
Number of extensions: 9
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: 350
Length adjustment: 29
Effective length of query: 321
Effective length of database: 321
Effective search space:   103041
Effective search space used:   103041
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 5208339 Shew_0851 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
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.30630.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   5.2e-175  567.1   0.0   5.9e-175  566.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5208339  Shew_0851 phospho-2-dehydro-3-de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208339  Shew_0851 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.9   0.0  5.9e-175  5.9e-175       1     342 []       6     349 ..       6     349 .. 0.99

  Alignments for each domain:
  == domain 1  score: 566.9 bits;  conditional E-value: 5.9e-175
                        TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaekl 78 
                                      dd+ri ki+ell+P ++ ++fp++e+a ++v ++r++i++il+ +ddrllv+iGPcsihdp+aaley +rl+kl+e++
  lcl|FitnessBrowser__PV4:5208339   6 DDVRINKIKELLPPVAILERFPASENASATVFNARQNIHNILKKEDDRLLVIIGPCSIHDPKAALEYGERLAKLREQY 83 
                                      799*************************************************************************** PP

                        TIGR00034  79 kddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswga 156
                                      kd+le+vmrvyfekPrttvGWkGlindP++++sf++n+Glr arkllldl+elg+p+a+e+ld+i+pqy+adl++wga
  lcl|FitnessBrowser__PV4:5208339  84 KDQLEVVMRVYFEKPRTTVGWKGLINDPYMDNSFKLNDGLRTARKLLLDLNELGVPTAGEFLDMITPQYVADLMCWGA 161
                                      ****************************************************************************** PP

                        TIGR00034 157 iGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkp 234
                                      iGarttesqvhrelasgls+pvgfkngtdG++kvaidai aa+a+h+flsvtk G++aiv+tkGn+d+hiilrGGk+p
  lcl|FitnessBrowser__PV4:5208339 162 IGARTTESQVHRELASGLSCPVGFKNGTDGTIKVAIDAIGAASAPHHFLSVTKYGHSAIVSTKGNPDCHIILRGGKEP 239
                                      ****************************************************************************** PP

                        TIGR00034 235 nydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..kee 310
                                      ny+ae+v+++ e+l ka+l +++m+dfsh+ns+k++krq+ v e+v++q++ Ge+ai+Gvm+es+l+eG+q+   +++
  lcl|FitnessBrowser__PV4:5208339 240 NYSAEHVQAISEQLAKANLPQNIMVDFSHANSSKQFKRQMLVGEDVASQVSAGERAIFGVMVESHLVEGRQDYieGQP 317
                                      ************************************************************************878899 PP

                        TIGR00034 311 lkyGksvtdacigwedteallrklaeavkerr 342
                                      l yG+s+tdacigwedte+ll++l++ v err
  lcl|FitnessBrowser__PV4:5208339 318 LCYGQSITDACIGWEDTETLLANLNRCVLERR 349
                                      *************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (350 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: 7.40
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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