Alignments for a candidate for aroG in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Dechloromonas agitata is5

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_027458324.1 K420_RS0112295 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::P00888
         (356 letters)



>NCBI__GCF_000519045.1:WP_027458324.1
          Length = 357

 Score =  369 bits (946), Expect = e-107
 Identities = 181/352 (51%), Positives = 240/352 (68%), Gaps = 1/352 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           L N++++    + TP ++ A  P+S +    ++  R  +  I+  +D RL VV GPCSIH
Sbjct: 6   LENINVSAFDSMPTPAEIHAKLPISDKAARTVSHGRNLLRKILDRKDHRLFVVVGPCSIH 65

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           DP   L+YA R K LA EV D+L ++MRVYFEKPRTTVGWKG INDP MD SF V  G++
Sbjct: 66  DPVAGLDYAHRLKKLADEVGDTLQIIMRVYFEKPRTTVGWKGYINDPFMDDSFQVNVGME 125

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
            AR+ LL++  +GLP  TEALDP  PQY GDL +W+AIGARTTESQTHREM+SGLS PVG
Sbjct: 126 KAREFLLQVNEIGLPAGTEALDPYGPQYYGDLIAWTAIGARTTESQTHREMSSGLSTPVG 185

Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244
           FKN T G L  A NA+ +A++PH F+G+N  G+VA+++T GNP GH++LRGG++ PNY  
Sbjct: 186 FKNATSGDLTVATNAILSASRPHSFLGLNNEGRVAIVRTTGNPHGHIVLRGGESGPNYDT 245

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             +A  E  + +A L  +++VDCSH NS+K    QP V   VV QI+ GN+SI+G+MIES
Sbjct: 246 VSIAMAEAAIAKAKLPANIVVDCSHANSSKKPELQPLVMADVVNQIRAGNKSILGVMIES 305

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTARVA 356
           NI  GNQ       ++KYG SVTD CI WE T+  +R+    L   L  R++
Sbjct: 306 NIEAGNQPIPADLKQLKYGCSVTDGCIGWETTEKTIRDAAVLLRDVLPERLS 357


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: 400
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: 357
Length adjustment: 29
Effective length of query: 327
Effective length of database: 328
Effective search space:   107256
Effective search space used:   107256
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_027458324.1 K420_RS0112295 (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.29435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-145  468.0   0.0   8.7e-145  467.7   0.0    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027458324.1  K420_RS0112295 3-deoxy-7-phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027458324.1  K420_RS0112295 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.0  8.7e-145  8.7e-145       2     335 ..       8     345 ..       7     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 8.7e-145
                                 TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 
                                               ++++ ++d++ tP+e++ak p++ kaa +v + r+ + +il+ kd+rl+vv+GPcsihdp a l+ya+r
  lcl|NCBI__GCF_000519045.1:WP_027458324.1   8 NINVSAFDSMPTPAEIHAKLPISDKAARTVSHGRNLLRKILDRKDHRLFVVVGPCSIHDPVAGLDYAHR 76 
                                               788999*************************************************************** PP

                                 TIGR00034  71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139
                                               lkkla+++ d l+i+mrvyfekPrttvGWkG indP +++sf+vn G++ ar++ll+++e+glp++te+
  lcl|NCBI__GCF_000519045.1:WP_027458324.1  77 LKKLADEVGDTLQIIMRVYFEKPRTTVGWKGYINDPFMDDSFQVNVGMEKAREFLLQVNEIGLPAGTEA 145
                                               ********************************************************************* PP

                                 TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208
                                               ld+  pqy++dl++w+aiGarttesq+hre++sgls pvgfkn+t G+l va +ai +a+++h fl+ +
  lcl|NCBI__GCF_000519045.1:WP_027458324.1 146 LDPYGPQYYGDLIAWTAIGARTTESQTHREMSSGLSTPVGFKNATSGDLTVATNAILSASRPHSFLGLN 214
                                               ********************************************************************* PP

                                 TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276
                                               ++G+vaiv+t+Gn++ghi+lrGG++ pnyd+ ++a +++ + ka+l +++++d+sh+ns+k+ + q+ v
  lcl|NCBI__GCF_000519045.1:WP_027458324.1 215 NEGRVAIVRTTGNPHGHIVLRGGESgPNYDTVSIAMAEAAIAKAKLPANIVVDCSHANSSKKPELQPLV 283
                                               ********************************************************************* PP

                                 TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrkla 335
                                               +++vv+qi+ G+k+i+Gvmiesn+e Gnq +    ++lkyG+svtd cigwe+te+ +r+ a
  lcl|NCBI__GCF_000519045.1:WP_027458324.1 284 MADVVNQIRAGNKSILGVMIESNIEAGNQPIpadLKQLKYGCSVTDGCIGWETTEKTIRDAA 345
                                               ******************************965457899*****************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (357 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.45
//
[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