Alignments for a candidate for aroB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Shewanella oneidensis MR-1

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 199482 SO0287 3-dehydroquinate synthase (NCBI ptt file)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__MR1:199482
          Length = 359

 Score =  429 bits (1104), Expect = e-125
 Identities = 216/358 (60%), Positives = 271/358 (75%), Gaps = 2/358 (0%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAG 61
           ++I V LGERSYPI I   L ++  +       +++++VTNET+APLYL +V+  +   G
Sbjct: 3   QQIQVDLGERSYPIYIGQSLMSDSETLSRYLLKKRILIVTNETVAPLYLKQVQDTMASFG 62

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
             + SVIL DGEQ+K L  LD++FTALLQ+ +GRD+ LVALGGGV+GD+TGFAAA YQRG
Sbjct: 63  -EISSVILSDGEQFKDLTHLDSIFTALLQRNYGRDSVLVALGGGVIGDMTGFAAACYQRG 121

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
           + FIQ+PTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQP  V++D +CL+TLP RE A+G
Sbjct: 122 IDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPQIVIIDTECLQTLPAREFAAG 181

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
           +AEVIKYGI+ D  FF WLE N+ AL  LD  A+ Y I RCCE+KA+VV+ DE E G+RA
Sbjct: 182 MAEVIKYGIMWDADFFQWLENNVQALKSLDTQALVYAISRCCEIKADVVSQDETEQGVRA 241

Query: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301
           LLNLGHTFGHAIEAEMGYGNWLHGEAVAAG V+AA+T++ LG    +   RI+ LL+   
Sbjct: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGTVLAAQTAKSLGLIDESIVCRIVQLLQAFD 301

Query: 302 LPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADC 359
           LPV  P  M  ++++ HM RDKKVL G++RL+LP AIG++EV S V  E  L  +  C
Sbjct: 302 LPVKAPESMDFESFIQHMRRDKKVLGGQIRLVLPTAIGRAEVFSQVP-ESTLEQVICC 358


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: 328
Number of extensions: 5
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: 362
Length of database: 359
Length adjustment: 29
Effective length of query: 333
Effective length of database: 330
Effective search space:   109890
Effective search space used:   109890
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 199482 SO0287 (3-dehydroquinate synthase (NCBI ptt file))
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.18515.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.5e-126  406.6   0.0   5.1e-126  406.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:199482  SO0287 3-dehydroquinate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199482  SO0287 3-dehydroquinate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.5   0.0  5.1e-126  5.1e-126       1     342 [.      14     355 ..      14     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 406.5 bits;  conditional E-value: 5.1e-126
                       TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlle 77 
                                     y++++g++l++   e+l++   +++++++t+e+v+ l+ ++++++ +s   e+  ++++dge+ K+l+++ ++ ++ll+
  lcl|FitnessBrowser__MR1:199482  14 YPIYIGQSLMSDS-ETLSRylLKKRILIVTNETVAPLYLKQVQDTMAS-FGEISSVILSDGEQFKDLTHLDSIFTALLQ 90 
                                     6789999998854.5555546679**********************99.779999************************ PP

                       TIGR01357  78 eklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlkv 156
                                     ++  r+svlva+GGGv+gD++GF+Aa y+RGi+++q+PTtll++vDssvGGKt++n+plgkN+iGafyqP+ V+id+++
  lcl|FitnessBrowser__MR1:199482  91 RNYGRDSVLVALGGGVIGDMTGFAAACYQRGIDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPQIVIIDTEC 169
                                     ******************************************************************************* PP

                       TIGR01357 157 letlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalLNfGH 235
                                     l+tlp re+++GmaEviK+g+++da++f++le+n ++l++l +++al  +i+r++e+Ka+vV++De+e+g+RalLN+GH
  lcl|FitnessBrowser__MR1:199482 170 LQTLPAREFAAGMAEVIKYGIMWDADFFQWLENNVQALKSL-DTQALVYAISRCCEIKADVVSQDETEQGVRALLNLGH 247
                                     ***********************************988765.66*********************************** PP

                       TIGR01357 236 tlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkDKKne 313
                                     t+gHaiEa+++y+ + HGeaVa G v++a+++++lgl++++++ r+v+ll+++ lp+k ++++++e++++++ +DKK  
  lcl|FitnessBrowser__MR1:199482 248 TFGHAIEAEMGYGnWLHGEAVAAGTVLAAQTAKSLGLIDESIVCRIVQLLQAFDLPVKAPESMDFESFIQHMRRDKKVL 326
                                     ******************************************************************************* PP

                       TIGR01357 314 gskiklvlleeiGkaalasevteeellea 342
                                     g++i+lvl+++iG+a++ s+v+e++l ++
  lcl|FitnessBrowser__MR1:199482 327 GGQIRLVLPTAIGRAEVFSQVPESTLEQV 355
                                     *********************99888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.25
//
[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