Alignments for a candidate for aroB in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Caulobacter crescentus NA1000

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate CCNA_03104 CCNA_03104 3-dehydroquinate synthase

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__Caulo:CCNA_03104
          Length = 370

 Score =  301 bits (772), Expect = 1e-86
 Identities = 171/351 (48%), Positives = 221/351 (62%), Gaps = 7/351 (1%)

Query: 4   IVVTLGERSYPITIASGLFNEPASFLPLKSGEQ--VMLVTNETLAPLYLDKVRGVLEQAG 61
           + V LGER+Y + I  GL ++    +    G++  V +VT+  +   + +++   L+ AG
Sbjct: 5   VPVGLGERAYDVVIGPGLLDQAGERVAAVLGKRKRVAVVTDAHVGAHHGERLSAALQGAG 64

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
           + VD + +  GE+ KS   L  +   LL     R   +VALGGGVVGDL GFAAA Y+RG
Sbjct: 65  ITVDLITIAPGEESKSFEGLADLSDRLLALNLERGDQIVALGGGVVGDLAGFAAAIYKRG 124

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
           + F+QVPTTLL+QVDSSVGGKTA++ P GKN+IGAF+QP  V+ DLD L TLP RELA G
Sbjct: 125 IDFVQVPTTLLAQVDSSVGGKTAIDTPRGKNLIGAFHQPRLVLADLDVLATLPARELACG 184

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
            AE+IKYG++ D AFF WLE N+ A+L  D  A+   + R  E+KAE+VA DE+E G RA
Sbjct: 185 YAEIIKYGLLGDFAFFEWLETNVQAVLDRDVDALVRAVGRSVEMKAEIVAEDEKEAGRRA 244

Query: 242 LLNLGHTFGHAIEAEMGYGNWL-HGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           LLNLGHTFGHAIEAEMG+G  L HGEAV  GM  A R S RLG   S +  R    +K A
Sbjct: 245 LLNLGHTFGHAIEAEMGFGEALKHGEAVGVGMAQAFRFSARLGLCPSQDAVRAQAAIKAA 304

Query: 301 GLPVN----GPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGV 347
           GLP       P   SA A + H  +DKK   G++  +L   IG + V   V
Sbjct: 305 GLPTTLADVRPEPFSADALIAHCGQDKKAQGGKLTFVLARGIGDAFVAKDV 355


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: 308
Number of extensions: 11
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: 362
Length of database: 370
Length adjustment: 30
Effective length of query: 332
Effective length of database: 340
Effective search space:   112880
Effective search space used:   112880
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 CCNA_03104 CCNA_03104 (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.22575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-124  402.1   0.0   1.3e-124  401.9   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03104  CCNA_03104 3-dehydroquinate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03104  CCNA_03104 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.9   0.0  1.3e-124  1.3e-124       1     338 [.      14     359 ..      14     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 401.9 bits;  conditional E-value: 1.3e-124
                             TIGR01357   1 ykvkvgegllkklveelae...kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvak 70 
                                           y+v++g gll+++ e +a    k++++ v+td +v ++++e+l++al+ +g++v+ +++ +geesKs+e +a+
  lcl|FitnessBrowser__Caulo:CCNA_03104  14 YDVVIGPGLLDQAGERVAAvlgKRKRVAVVTDAHVGAHHGERLSAALQGAGITVDLITIAPGEESKSFEGLAD 86 
                                           789*************999886669************************************************ PP

                             TIGR01357  71 lldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGa 143
                                           l d+ll+ +ler +++va+GGGvvgDlaGF+Aa+y+RGi++vqvPTtlla+vDssvGGKt+i++p+gkNliGa
  lcl|FitnessBrowser__Caulo:CCNA_03104  87 LSDRLLALNLERGDQIVALGGGVVGDLAGFAAAIYKRGIDFVQVPTTLLAQVDSSVGGKTAIDTPRGKNLIGA 159
                                           ************************************************************************* PP

                             TIGR01357 144 fyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKae 216
                                           f+qP++Vl dl+vl+tlp rel++G+aE+iK+gl+ d ++fe+le+n +++l++ + +al +++ rs+e+Kae
  lcl|FitnessBrowser__Caulo:CCNA_03104 160 FHQPRLVLADLDVLATLPARELACGYAEIIKYGLLGDFAFFEWLETNVQAVLDR-DVDALVRAVGRSVEMKAE 231
                                           *************************************************99985.77**************** PP

                             TIGR01357 217 vVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgllkaellerlvallkkl 287
                                           +V+eDeke+g RalLN+GHt+gHaiEa+++++  l+HGeaV +Gm++++++s +lgl++++++ r +a +k++
  lcl|FitnessBrowser__Caulo:CCNA_03104 232 IVAEDEKEAGRRALLNLGHTFGHAIEAEMGFGeaLKHGEAVGVGMAQAFRFSARLGLCPSQDAVRAQAAIKAA 304
                                           ******************************9999*************************************** PP

                             TIGR01357 288 glptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevteee 338
                                           glpt+l +     +s+++l++++ +DKK++g+k+++vl++ iG+a++a++v++ +
  lcl|FitnessBrowser__Caulo:CCNA_03104 305 GLPTTLADvrpePFSADALIAHCGQDKKAQGGKLTFVLARGIGDAFVAKDVDRAA 359
                                           *******999999***********************************8885544 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (370 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: 12.19
//
[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