Alignments for a candidate for aroB in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Klebsiella variicola At-22

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_008807017.1 KVAR_RS01695 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>NCBI__GCF_000025465.1:WP_008807017.1
          Length = 364

 Score =  638 bits (1645), Expect = 0.0
 Identities = 320/362 (88%), Positives = 340/362 (93%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           MER+ VTLGERSYPITIA+GLFN+PASFLPLKSG+Q MLVTNETLAPLYLD VR VLEQA
Sbjct: 1   MERLTVTLGERSYPITIAAGLFNDPASFLPLKSGDQAMLVTNETLAPLYLDTVRSVLEQA 60

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
           GVNVDSVILPDGEQYKSLAV+DTVFTALLQKPHGRDTTLVALGGGV+GDLTGFAAASYQR
Sbjct: 61  GVNVDSVILPDGEQYKSLAVMDTVFTALLQKPHGRDTTLVALGGGVIGDLTGFAAASYQR 120

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAF+QP SVVVDL+CLKTLP RELAS
Sbjct: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFWQPVSVVVDLNCLKTLPARELAS 180

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           GLAEVIKYG+ILDG FF+WLE N+DALL LD  AMAYCIRRCCELKAEVVAADERETGLR
Sbjct: 181 GLAEVIKYGVILDGEFFSWLENNIDALLALDEKAMAYCIRRCCELKAEVVAADERETGLR 240

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAA TSERLGQF + +TQRII LLKRA
Sbjct: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAAHTSERLGQFRAQDTQRIIDLLKRA 300

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360
           GLPV GP+EMSAQAYLPHM+RDKKVLAG+MRL+LPLAIG SE+R GV H++VL AIAD Q
Sbjct: 301 GLPVRGPQEMSAQAYLPHMMRDKKVLAGDMRLVLPLAIGSSELRGGVPHDVVLGAIADTQ 360

Query: 361 SA 362
            A
Sbjct: 361 QA 362


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: 496
Number of extensions: 7
Number of successful extensions: 1
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: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
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_008807017.1 KVAR_RS01695 (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.449577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-126  408.0   0.0   1.9e-126  407.9   0.0    1.0  1  NCBI__GCF_000025465.1:WP_008807017.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_008807017.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   0.0  1.9e-126  1.9e-126       1     339 [.      13     352 ..      13     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 1.9e-126
                             TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakll 72 
                                           y++++  gl++  ++ l   + ++++++t+e+++ l+ ++++++l+++gv+v+ +++pdge++Ksl+++ ++ 
  NCBI__GCF_000025465.1:WP_008807017.1  13 YPITIAAGLFNDPASFLPLkSGDQAMLVTNETLAPLYLDTVRSVLEQAGVNVDSVILPDGEQYKSLAVMDTVF 85 
                                           57889999999777777763459************************************************** PP

                             TIGR01357  73 dqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafy 145
                                           ++ll++ + r+++lva+GGGv+gDl+GF+Aa+y+RG+r++qvPTtll++vDssvGGKt++n+plgkN+iGaf+
  NCBI__GCF_000025465.1:WP_008807017.1  86 TALLQKPHGRDTTLVALGGGVIGDLTGFAAASYQRGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFW 158
                                           ************************************************************************* PP

                             TIGR01357 146 qPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevV 218
                                           qP  V++dl++l+tlp rel++G+aEviK+g+i d e+f++le+n ++ll l+e +a++ +i+r++e+KaevV
  NCBI__GCF_000025465.1:WP_008807017.1 159 QPVSVVVDLNCLKTLPARELASGLAEVIKYGVILDGEFFSWLENNIDALLALDE-KAMAYCIRRCCELKAEVV 230
                                           ***********************************************9998655.****************** PP

                             TIGR01357 219 eeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglp 290
                                           ++De+e+glRalLN+GHt+gHaiEa+++y+ + HGeaVa Gmv++a++se+lg+++a++++r+++llk++glp
  NCBI__GCF_000025465.1:WP_008807017.1 231 AADERETGLRALLNLGHTFGHAIEAEMGYGnWLHGEAVAAGMVMAAHTSERLGQFRAQDTQRIIDLLKRAGLP 303
                                           ************************************************************************* PP

                             TIGR01357 291 tklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339
                                           ++ ++++s++++l ++++DKK  ++ ++lvl+ +iG+ +l+  v+++ +
  NCBI__GCF_000025465.1:WP_008807017.1 304 VRGPQEMSAQAYLPHMMRDKKVLAGDMRLVLPLAIGSSELRGGVPHDVV 352
                                           *************************************999877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (364 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.79
//
[ok]

This GapMind analysis is from Jul 25 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 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