Alignments for a candidate for aroB in Caldicellulosiruptor kronotskyensis 2002

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Caldicellulosiruptor kronotskyensis 2002

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_013430318.1 CALKRO_RS06850 3-dehydroquinate synthase

Query= curated2:Q894C9
         (373 letters)



>NCBI__GCF_000166775.1:WP_013430318.1
          Length = 361

 Score =  225 bits (573), Expect = 2e-63
 Identities = 126/322 (39%), Positives = 191/322 (59%), Gaps = 11/322 (3%)

Query: 52  SEMFLITDDKVYSIYKDRIEMLKNIYNIKEFYFKNGEENKTLETLQEIYSFLMENNAKRN 111
           S + + TD  VY +YKD I+ L   Y    + F  GEE+K++E+  +   +L++ N  R 
Sbjct: 37  SNLVIFTDKMVYRLYKDFIDSLSYSYL---YLFDEGEESKSIESYLKAIDYLLDRNVDRR 93

Query: 112 SIIIALGGGVVGDLVGFVASTYMRGVRYINIPTTLLSQIDSCVGGKVGYNYKGIKNLIGS 171
           ++ +A+GGGV+GD+VGF+ASTY RGV+ I+IPTTLLS +DS +GGK G N+K  KN IG+
Sbjct: 94  ALFVAIGGGVIGDVVGFIASTYKRGVKLIHIPTTLLSMVDSSIGGKTGINHKSYKNQIGT 153

Query: 172 FYNPEFVFISTNFLKTLDFQRFKDGLGEVIKYGLILDEEIISFIEENYKGVLEKESDKLL 231
           FY PE + IS  FL+TL       G GE+IKYG  LD+ I+   +     V E   DK+L
Sbjct: 154 FYQPEMIIISPKFLETLPKSEILSGFGEIIKYGFTLDKSILDMKDRFENDVFEIFQDKIL 213

Query: 232 --YITRTCLILKKQVIEMDYKDLGFRNILNFGHTIGHAIEMTSKNKITHGEAVALGMLVS 289
              + +  +  K +V+E D K+   R +LNFGHT+GHA+E       +HG  V  GM+  
Sbjct: 214 AMQLIKKSINCKVEVVENDEKESHLREVLNFGHTVGHALETYYNYHFSHGIFVIFGMVAE 273

Query: 290 LKLSEHIYGLD-KNLYYRMEKLYK-KLGLPTKYKVDNYNLFMYAINHDKKN-KDNIRFVL 346
           + LS  ++  D  NL + +  L K  + LP +++       +  + +DKKN   +IR VL
Sbjct: 274 MILSNILFNFDLSNLDFLIRILEKNNIKLPQRFEKSQ---IISIMKYDKKNINASIRMVL 330

Query: 347 LKDVEKPEVKIEVNKEEILKAI 368
           LKDV    +  +++++ + KA+
Sbjct: 331 LKDVCDYVLGHKIDEDVLYKAL 352


Lambda     K      H
   0.320    0.141    0.393 

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: 473
Number of extensions: 23
Number of successful extensions: 3
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: 373
Length of database: 361
Length adjustment: 30
Effective length of query: 343
Effective length of database: 331
Effective search space:   113533
Effective search space used:   113533
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_013430318.1 CALKRO_RS06850 (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.2187372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-106  342.9   0.1   1.3e-106  342.6   0.1    1.0  1  NCBI__GCF_000166775.1:WP_013430318.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430318.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.6   0.1  1.3e-106  1.3e-106       9     338 ..      23     347 ..      17     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 342.6 bits;  conditional E-value: 1.3e-106
                             TIGR01357   9 llkklveelaeka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleekl 80 
                                            ++k+ e+la+++ s+lv++td+ v++l+++ ++++  s     + +++ +geesKs+e++ k +d+ll++++
  NCBI__GCF_000166775.1:WP_013430318.1  23 SIEKTGEYLASFNcSNLVIFTDKMVYRLYKDFIDSLSYS-----YLYLFDEGEESKSIESYLKAIDYLLDRNV 90 
                                           5677889999955599*************9999998866.....899************************** PP

                             TIGR01357  81 erksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlid 153
                                           +r+ + vaiGGGv+gD++GF+A+ty+RG++l+++PTtll+mvDss+GGKtgin++  kN iG+fyqP++++i+
  NCBI__GCF_000166775.1:WP_013430318.1  91 DRRALFVAIGGGVIGDVVGFIASTYKRGVKLIHIPTTLLSMVDSSIGGKTGINHKSYKNQIGTFYQPEMIIIS 163
                                           ************************************************************************* PP

                             TIGR01357 154 lkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleal.eelikrsievKaevVeeDekes 225
                                           +k+letlp+ e+ +G++E+iK+g+  d+++++   ++e+++ ++ + ++l  +lik+si++K evVe+Dekes
  NCBI__GCF_000166775.1:WP_013430318.1 164 PKFLETLPKSEILSGFGEIIKYGFTLDKSILDMKDRFENDVFEIFQDKILaMQLIKKSINCKVEVVENDEKES 236
                                           **************************************998888776665269******************** PP

                             TIGR01357 226 glRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkkls 298
                                            lR++LNfGHt+gHa+E+ ++y++sHG  V++Gmv e+ ls+ l +++ ++l+ l+++l+k   ++kl+++++
  NCBI__GCF_000166775.1:WP_013430318.1 237 HLREVLNFGHTVGHALETYYNYHFSHGIFVIFGMVAEMILSNILFNFDLSNLDFLIRILEKN--NIKLPQRFE 307
                                           ***********************************************************998..566777789 PP

                             TIGR01357 299 veellkallkDKKnegskiklvlleeiGkaalasevteee 338
                                            +++++ +++DKKn + +i++vll+++ + +l ++++e+ 
  NCBI__GCF_000166775.1:WP_013430318.1 308 KSQIISIMKYDKKNINASIRMVLLKDVCDYVLGHKIDEDV 347
                                           9**************************9999887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (361 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: 00:00:00.00
# Mc/sec: 14.23
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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