Alignments for a candidate for aroG in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Synechococcus elongatus PCC 7942

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Synpcc7942_2501 Synpcc7942_2501 phospho-2-dehydro-3-heoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__SynE:Synpcc7942_2501
          Length = 354

 Score =  388 bits (996), Expect = e-112
 Identities = 183/344 (53%), Positives = 246/344 (71%), Gaps = 1/344 (0%)

Query: 7   NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66
           +++H+ + + L++P ++    PLS      +A +R  +  I+   D RLLV+ GPCSIHD
Sbjct: 5   SDLHVVETRSLISPAEIHQKLPLSETAADLVASTRDRVRSILRNSDRRLLVIVGPCSIHD 64

Query: 67  PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126
              A +Y ++   L  E++D L +VMRVYFEKPRTTVGWKGLINDPH+DGS+D+  G+Q 
Sbjct: 65  VNAAYDYGQKLLPLREELADELEIVMRVYFEKPRTTVGWKGLINDPHLDGSYDINTGIQR 124

Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186
           ARKLLL L +MGLP ATE LDP  PQY+ D+ +W+AIGARTTESQTHREMASGLSMP+GF
Sbjct: 125 ARKLLLGLADMGLPAATELLDPIIPQYIADVIAWTAIGARTTESQTHREMASGLSMPIGF 184

Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPA 245
           KNGTDGS   A NAM +A+QPH F+GIN  G  +++ T GNPDGH++LRGG K PNY+ A
Sbjct: 185 KNGTDGSFHIAANAMLSASQPHHFLGINHDGLASIVSTTGNPDGHLVLRGGSKGPNYAAA 244

Query: 246 DVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESN 305
           D+ +   ++   GL   +MVDCSHGNSNKDYRRQ  V   +  Q+ +G+R ++G+MIES+
Sbjct: 245 DIEEAAYQLASMGLHARVMVDCSHGNSNKDYRRQSVVLSDLAEQVAEGSRHLMGVMIESH 304

Query: 306 IHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNG 349
           + EGNQ      SE++YG S+TD C+ +  T+ +LRE+ +   G
Sbjct: 305 LVEGNQPIPADLSELRYGQSITDPCVDFPTTEKMLRELARAQRG 348


Lambda     K      H
   0.316    0.131    0.378 

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: 409
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: 356
Length of database: 354
Length adjustment: 29
Effective length of query: 327
Effective length of database: 325
Effective search space:   106275
Effective search space used:   106275
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate Synpcc7942_2501 Synpcc7942_2501 (phospho-2-dehydro-3-heoxyheptonate 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.24252.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-154  498.5   0.0   4.4e-154  498.3   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2501  Synpcc7942_2501 phospho-2-dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2501  Synpcc7942_2501 phospho-2-dehydro-3-heoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.3   0.0  4.4e-154  4.4e-154       2     337 ..       6     345 ..       5     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 498.3 bits;  conditional E-value: 4.4e-154
                                 TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 
                                               dl++v+  +l++P+e+++k pl+e+aa+ va++r+++  il+ +d rllv++GPcsihd +aa++y ++
  lcl|FitnessBrowser__SynE:Synpcc7942_2501   6 DLHVVETRSLISPAEIHQKLPLSETAADLVASTRDRVRSILRNSDRRLLVIVGPCSIHDVNAAYDYGQK 74 
                                               78899999************************************************************* PP

                                 TIGR00034  71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139
                                               l +l+e+l d+leivmrvyfekPrttvGWkGlindP+l++s+d+n+G++ arklll l+++glp+atel
  lcl|FitnessBrowser__SynE:Synpcc7942_2501  75 LLPLREELADELEIVMRVYFEKPRTTVGWKGLINDPHLDGSYDINTGIQRARKLLLGLADMGLPAATEL 143
                                               ********************************************************************* PP

                                 TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208
                                               ld+i+pqy+ad+++w+aiGarttesq+hre+asgls+p+gfkngtdGs ++a +a+ +a+++h+fl+++
  lcl|FitnessBrowser__SynE:Synpcc7942_2501 144 LDPIIPQYIADVIAWTAIGARTTESQTHREMASGLSMPIGFKNGTDGSFHIAANAMLSASQPHHFLGIN 212
                                               ********************************************************************* PP

                                 TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                               ++G ++iv+t+Gn+dgh++lrGG k pny a+d++e+  +l  +gl++++m+d+shgnsnkdy+rq  v
  lcl|FitnessBrowser__SynE:Synpcc7942_2501 213 HDGLASIVSTTGNPDGHLVLRGGSKgPNYAAADIEEAAYQLASMGLHARVMVDCSHGNSNKDYRRQSVV 281
                                               *************************9******************************************* PP

                                 TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaea 337
                                                ++++eq+aeG++ ++Gvmies+l+eGnq +    +el yG+s+td c+++ +te++lr+la+a
  lcl|FitnessBrowser__SynE:Synpcc7942_2501 282 LSDLAEQVAEGSRHLMGVMIESHLVEGNQPIpadLSELRYGQSITDPCVDFPTTEKMLRELARA 345
                                               ******************************965457899**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (354 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: 9.45
//
[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