Alignments for a candidate for aroB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate CA265_RS11615 CA265_RS11615 3-dehydroquinate synthase

Query= curated2:A6LEZ7
         (353 letters)



>FitnessBrowser__Pedo557:CA265_RS11615
          Length = 352

 Score =  260 bits (664), Expect = 4e-74
 Identities = 149/335 (44%), Positives = 196/335 (58%), Gaps = 8/335 (2%)

Query: 16  LQDFLSSLKYDKLFILMDTNTKEKCFPLVEDI-PAFQKAPILVMEAGDMNKGFVSLAQIW 74
           L+  L S KY K+F+L D +T E C PL + +   F +  ++   AG+ NK       IW
Sbjct: 20  LKTLLESNKYSKVFVLADEHTSEICLPLFQSLLDDFSEFDLIETSAGEENKNIDFCIGIW 79

Query: 75  TALSNEGASRNSLLVNLGGGMITDMGGFAGATFKRGIRTINIPTTLMASVDAAVGGKTGI 134
             L +  A R SL++NLGGG+ITDMGGF  +T+KRGI  IN+PTTL++ VDA+VGGKTGI
Sbjct: 80  KTLLDFEADRKSLMINLGGGVITDMGGFIASTYKRGIDFINVPTTLLSQVDASVGGKTGI 139

Query: 135 NFNGLKNEVGSFYPPLCVFIDCDFLRTLDRDNILSGYAEMIKHGLISSMENYASVMLFDI 194
           + + +KN VG+F  P  VFI+  FL+TL +  +LSG+AEMIKHGLI     Y       +
Sbjct: 140 DIDNVKNMVGTFTLPQMVFIETAFLKTLPQRELLSGFAEMIKHGLIYDKPYYEK-----L 194

Query: 195 DTMNYSYLNSL-VGQSVAVKERIVEEDPKEQGIRKALNFGHTIGHAFESLSFLK-MRPIL 252
              NY   ++  + +SV +K  +V  DP E+ +RK LNFGHTIGHA E  S      P+ 
Sbjct: 195 KESNYLTPSAEDIYRSVEIKNEVVTIDPHEKNLRKILNFGHTIGHAVEGYSLANDENPLT 254

Query: 253 HGHAVAAGIVSELYLSHKLCGFPMEKLSQVVYYIKEYYPALFFDCTDYDTLYELMTHDKK 312
           HG A+A G V E  LS K       +L  +  YI   YP        +DTL ELM  DKK
Sbjct: 255 HGEAIAIGFVCEAALSIKNSTLTQAELKDISEYILSLYPKYHIKKESFDTLLELMQSDKK 314

Query: 313 NEGGIINFTLLKNVGDVRINQSVTKEKILESLDFY 347
           NE G I F+LL+  G    N  V+   IL SLD+Y
Sbjct: 315 NEDGNILFSLLETTGKCTFNCRVSTADILSSLDYY 349


Lambda     K      H
   0.321    0.139    0.402 

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: 393
Number of extensions: 15
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: 353
Length of database: 352
Length adjustment: 29
Effective length of query: 324
Effective length of database: 323
Effective search space:   104652
Effective search space used:   104652
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 CA265_RS11615 CA265_RS11615 (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.2153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.1e-107  344.3   0.0   4.9e-107  344.0   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS11615  CA265_RS11615 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS11615  CA265_RS11615 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.0   0.0  4.9e-107  4.9e-107      13     341 ..      20     344 ..      10     347 .. 0.93

  Alignments for each domain:
  == domain 1  score: 344.0 bits;  conditional E-value: 4.9e-107
                                  TIGR01357  13 lveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleek 79 
                                                l + l++ k sk++v+ de++++++   ++++l +  +e + +  ++gee+K+++ +  ++++ll+ +
  lcl|FitnessBrowser__Pedo557:CA265_RS11615  20 LKTLLESnKYSKVFVLADEHTSEICLPLFQSLLDD-FSEFDLIETSAGEENKNIDFCIGIWKTLLDFE 86 
                                                44455554569**********************88.9999**************************** PP

                                  TIGR01357  80 lerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqP 147
                                                ++rks+++++GGGv++D++GF+A+ty+RGi++++vPTtll++vD+svGGKtgi+ +++kN++G+f  P
  lcl|FitnessBrowser__Pedo557:CA265_RS11615  87 ADRKSLMINLGGGVITDMGGFIASTYKRGIDFINVPTTLLSQVDASVGGKTGIDIDNVKNMVGTFTLP 154
                                                ******************************************************************** PP

                                  TIGR01357 148 kaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKa 215
                                                ++V+i++++l+tlp+rel +G+aE+iKhgli+d+  +e+l++ + l          +e i rs+e+K+
  lcl|FitnessBrowser__Pedo557:CA265_RS11615 155 QMVFIETAFLKTLPQRELLSGFAEMIKHGLIYDKPYYEKLKESNYL-------TPSAEDIYRSVEIKN 215
                                                ****************************************996653.......3456789******** PP

                                  TIGR01357 216 evVeeDekesglRalLNfGHtlgHaiEallkyk....lsHGeaVaiGmvveaklseklgllkaeller 279
                                                evV+ D++e+ lR++LNfGHt+gHa+E  +  +    l+HGea+aiG v+ea ls k  +l + +l++
  lcl|FitnessBrowser__Pedo557:CA265_RS11615 216 EVVTIDPHEKNLRKILNFGHTIGHAVEGYSLANdenpLTHGEAIAIGFVCEAALSIKNSTLTQAELKD 283
                                                ***************************8765555689******************************* PP

                                  TIGR01357 280 lvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                                + +++ +l++++++kk  s+++ll+ +++DKKne+++i + lle  Gk++ +++v+  ++l+
  lcl|FitnessBrowser__Pedo557:CA265_RS11615 284 ISEYILSLYPKYHIKK-ESFDTLLELMQSDKKNEDGNILFSLLETTGKCTFNCRVSTADILS 344
                                                ********99999997.9**********************************9998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (352 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: 8.66
//
[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