Alignments for a candidate for aroG in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Malonomonas rubra DSM 5091

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_072904827.1 BUB13_RS00685 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P00888
         (356 letters)



>NCBI__GCF_900142125.1:WP_072904827.1
          Length = 347

 Score =  387 bits (995), Expect = e-112
 Identities = 192/341 (56%), Positives = 245/341 (71%), Gaps = 2/341 (0%)

Query: 7   NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66
           NN+++ +   ++ PE LK  FPL L+  A + DSR +I DI+ G D R++VV GPCSIHD
Sbjct: 5   NNINVREVTPIIAPEDLKQVFPLDLKDAAFVNDSRNAIKDILHGDDKRMIVVVGPCSIHD 64

Query: 67  PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126
           P+ A+EYA +  AL+ +V D L +VMRVYFEKPRTTVGWKGLINDP MDGS  +  GL I
Sbjct: 65  PKAAIEYAEKLAALSQKVQDKLLVVMRVYFEKPRTTVGWKGLINDPDMDGSHKISKGLGI 124

Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186
           AR+L  ++  + LP+A+E L+P  P YL D+ SW AIGARTTESQTHREMASGLS PVGF
Sbjct: 125 ARQLFSQITQLHLPIASEMLEPIIPHYLSDMISWGAIGARTTESQTHREMASGLSFPVGF 184

Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGK-APNYSPA 245
           KNGTDG L  A +AM AA   H F+GIN AG+ ++++T GNPD H++LRGG   PNYSP 
Sbjct: 185 KNGTDGGLKIATDAMAAARCSHSFLGINYAGRSSVVETTGNPDIHIVLRGGNDGPNYSPD 244

Query: 246 DVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESN 305
           D+A   + +++  L PS+MVDCSH NS K++ RQ  V +S+V QI  G  SI G+MIESN
Sbjct: 245 DIAATTELLKKNNLPPSIMVDCSHANSYKNHERQGEVLDSIVEQIATGTTSINGVMIESN 304

Query: 306 IHEGNQSSEQPRSEMKYGVSVTDACISWEMT-DALLREIHQ 345
           +  GNQS     S++KYGVSVTD C+ WE T D LLR  ++
Sbjct: 305 LKAGNQSIPDDLSQLKYGVSVTDKCVDWETTEDMLLRTFNR 345


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: 381
Number of extensions: 15
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: 347
Length adjustment: 29
Effective length of query: 327
Effective length of database: 318
Effective search space:   103986
Effective search space used:   103986
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 WP_072904827.1 BUB13_RS00685 (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.4169456.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-155  502.2   0.0   3.4e-155  501.9   0.0    1.0  1  NCBI__GCF_900142125.1:WP_072904827.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072904827.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.9   0.0  3.4e-155  3.4e-155       2     332 ..       6     340 ..       5     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 501.9 bits;  conditional E-value: 3.4e-155
                             TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 
                                           ++++ ++ ++++Pe+lk+ fpl  k a+ v++sr++i+dil+G+d+r++vv+GPcsihdp+aa+eya++l++l
  NCBI__GCF_900142125.1:WP_072904827.1   6 NINVREVTPIIAPEDLKQVFPLDLKDAAFVNDSRNAIKDILHGDDKRMIVVVGPCSIHDPKAAIEYAEKLAAL 78 
                                           6788999****************************************************************** PP

                             TIGR00034  75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147
                                           ++k++d+l +vmrvyfekPrttvGWkGlindPd+++s+++ kGl iar+l+ ++++l lp+a+e+l++i+p y
  NCBI__GCF_900142125.1:WP_072904827.1  79 SQKVQDKLLVVMRVYFEKPRTTVGWKGLINDPDMDGSHKISKGLGIARQLFSQITQLHLPIASEMLEPIIPHY 151
                                           ************************************************************************* PP

                             TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkG 220
                                           l+d++swgaiGarttesq+hre+asgls+pvgfkngtdG+lk+a da+ aa+ +h fl+++ aG++++vet+G
  NCBI__GCF_900142125.1:WP_072904827.1 152 LSDMISWGAIGARTTESQTHREMASGLSFPVGFKNGTDGGLKIATDAMAAARCSHSFLGINYAGRSSVVETTG 224
                                           ************************************************************************* PP

                             TIGR00034 221 nedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaii 292
                                           n+d hi+lrGG++ pny+++d+a+++e l+k +l +++m+d+sh+ns k+++rq ev +s+veqia+G ++i 
  NCBI__GCF_900142125.1:WP_072904827.1 225 NPDIHIVLRGGNDgPNYSPDDIAATTELLKKNNLPPSIMVDCSHANSYKNHERQGEVLDSIVEQIATGTTSIN 297
                                           ************************************************************************* PP

                             TIGR00034 293 GvmiesnleeGnqsl...keelkyGksvtdacigwedteallr 332
                                           Gvmiesnl+ Gnqs+    ++lkyG+svtd+c++we+te++l 
  NCBI__GCF_900142125.1:WP_072904827.1 298 GVMIESNLKAGNQSIpddLSQLKYGVSVTDKCVDWETTEDMLL 340
                                           ***************6444689*****************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (347 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.43
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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