Alignments for a candidate for aroB in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Magnetospirillum magneticum AMB-1

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011386279.1 AMB_RS19865 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_000009985.1:WP_011386279.1
          Length = 371

 Score =  313 bits (801), Expect = 6e-90
 Identities = 175/364 (48%), Positives = 228/364 (62%), Gaps = 4/364 (1%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFL-PLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           E ++V LGERSYPI I  GL +     + P   G + ++VT+  +AP YL++V+  L +A
Sbjct: 6   EEVMVELGERSYPIHIGPGLLDRAGELIKPKMRGGRALVVTDANVAPHYLERVQKSLAEA 65

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           GV     ++P GEQ K    L+ +  A+L+    R   +VALGGGVVGDLTGFAA+   R
Sbjct: 66  GVTTMHTVMPAGEQTKDFKHLEALLDAMLEARSERGIMVVALGGGVVGDLTGFAASILLR 125

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GV F+Q+PTTLLSQVDSSVGGKT +N   GKN+IG+FYQP  V+ D   L TLP R++ +
Sbjct: 126 GVDFVQIPTTLLSQVDSSVGGKTGINTRQGKNLIGSFYQPRLVLADTSVLNTLPRRQVLA 185

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           G AEV KYG+I D  FF WLEEN   ++  D  A  Y +   C  KA +V ADERE G+R
Sbjct: 186 GYAEVAKYGVIDDEPFFAWLEENGSKVVDGDLEARRYAVATSCRAKARIVGADEREGGVR 245

Query: 241 ALLNLGHTFGHAIEAEMGYG-NWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKR 299
           ALLNLGHTFGHA+EAE G+    LHGEAVA GMVMA R S RLG   +A+ +R+   L  
Sbjct: 246 ALLNLGHTFGHALEAETGFSEEMLHGEAVAIGMVMALRLSARLGLAPAADAERLERHLLA 305

Query: 300 AGLPVN--GPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIA 357
            GLPV    PR  +    + HM  DKKV  G++  ++   IGKS +   V    + + +A
Sbjct: 306 VGLPVTLPKPRLWAVDRLIHHMAGDKKVKDGKVTFVMAKGIGKSFLTRDVPEAELASMLA 365

Query: 358 DCQS 361
           +  S
Sbjct: 366 EMAS 369


Lambda     K      H
   0.320    0.136    0.392 

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: 337
Number of extensions: 14
Number of successful extensions: 4
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: 362
Length of database: 371
Length adjustment: 30
Effective length of query: 332
Effective length of database: 341
Effective search space:   113212
Effective search space used:   113212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_011386279.1 AMB_RS19865 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.7043.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-119  385.2   0.0   1.6e-119  385.0   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386279.1  AMB_RS19865 3-dehydroquinate syn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386279.1  AMB_RS19865 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.0   0.0  1.6e-119  1.6e-119       1     340 [.      17     361 ..      17     365 .. 0.97

  Alignments for each domain:
  == domain 1  score: 385.0 bits;  conditional E-value: 1.6e-119
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y++++g gll+++ e ++   +  +++v+td +v+ ++ e++++ l+++gv++++ v+p+ge++K++++
  lcl|NCBI__GCF_000009985.1:WP_011386279.1  17 YPIHIGPGLLDRAGELIKPkmRGGRALVVTDANVAPHYLERVQKSLAEAGVTTMHTVMPAGEQTKDFKH 85 
                                               689**************99644499******************************************** PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               +++lld++le+  er  ++va+GGGvvgDl+GF+A++ lRG+++vq+PTtll++vDssvGGKtgin+++
  lcl|NCBI__GCF_000009985.1:WP_011386279.1  86 LEALLDAMLEARSERGIMVVALGGGVVGDLTGFAASILLRGVDFVQIPTTLLSQVDSSVGGKTGINTRQ 154
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkNliG+fyqP++Vl d++vl+tlp+r++ +G+aEv K+g+i d+ +f++le+n +++++  +lea + 
  lcl|NCBI__GCF_000009985.1:WP_011386279.1 155 GKNLIGSFYQPRLVLADTSVLNTLPRRQVLAGYAEVAKYGVIDDEPFFAWLEENGSKVVD-GDLEARRY 222
                                               ********************************************************9997.578***** PP

                                 TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgll 272
                                               +++ s++ Ka++V +De+e g+RalLN+GHt+gHa+Ea+++++  + HGeaVaiGmv++++ls +lgl+
  lcl|NCBI__GCF_000009985.1:WP_011386279.1 223 AVATSCRAKARIVGADEREGGVRALLNLGHTFGHALEAETGFSeeMLHGEAVAIGMVMALRLSARLGLA 291
                                               ****************************************99999************************ PP

                                 TIGR01357 273 kaellerlvallkklglptklkk..klsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                               +a ++erl++ l ++glp++l+k   ++v+ l++++  DKK +++k+++v+++ iGk +l+++v+e el
  lcl|NCBI__GCF_000009985.1:WP_011386279.1 292 PAADAERLERHLLAVGLPVTLPKprLWAVDRLIHHMAGDKKVKDGKVTFVMAKGIGKSFLTRDVPEAEL 360
                                               **********************99899*********************************999988776 PP

                                 TIGR01357 340 l 340
                                                
  lcl|NCBI__GCF_000009985.1:WP_011386279.1 361 A 361
                                               5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (371 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.28
//
[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