Alignments for a candidate for aroB in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Ammonifex degensii KC4

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_015738684.1 ADEG_RS03370 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>NCBI__GCF_000024605.1:WP_015738684.1
          Length = 360

 Score =  332 bits (851), Expect = 9e-96
 Identities = 173/357 (48%), Positives = 243/357 (68%), Gaps = 3/357 (0%)

Query: 5   INVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGF 64
           + V L  +SY I +    L ++G+       G++++++SN T+   +G+V  +SLEAAG+
Sbjct: 4   VRVELGDRSYPIYVGEGLLARVGELTRQHLPGRRLMVISNSTVTGLYGEVLKESLEAAGW 63

Query: 65  QVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGI 124
           +V    +P GE +K L ++ +LYD+A+E  LER   ++A GGGV+GD+ GF AAT++RG+
Sbjct: 64  KVLWAEMPDGEEHKNLATVSRLYDLAVEGELERGDAILAFGGGVVGDVAGFVAATFMRGV 123

Query: 125 NVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGM 184
              QVPTTLLA VD+++GGK GVNHP GKNLIGAFHQPR V+ D   L++LP RE  +GM
Sbjct: 124 AWGQVPTTLLAQVDASVGGKVGVNHPQGKNLIGAFHQPRLVVADVDTLRSLPRREIASGM 183

Query: 185 AEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKEGGLR 244
           AEV+KYGVI  A  F  LE++  ++ L  + PE +   +  SC+ KA+VV  DEKE GLR
Sbjct: 184 AEVVKYGVIRSASFFAWLEEN--VEALLSLAPEALTHAVATSCRIKAEVVAADEKESGLR 241

Query: 245 AILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNA-LIEK 303
           AILN+GHTVGHA+E++T+Y    HGEAV IGMV A ++A  LGL   A+ +R+ A L+E 
Sbjct: 242 AILNFGHTVGHALEAMTDYVRFAHGEAVAIGMVVASRLARRLGLGFTAEEERRLANLLEA 301

Query: 304 AGLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQVL 360
            GLPT LP G D   ++  +Q DKKVK+GK+ F+LP  IG V +  EV  + + +VL
Sbjct: 302 IGLPTSLPPGTDPRELLLFMQRDKKVKEGKLTFILPRHIGEVEIVREVPQEILLEVL 358


Lambda     K      H
   0.319    0.136    0.388 

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: 375
Number of extensions: 16
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: 363
Length of database: 360
Length adjustment: 29
Effective length of query: 334
Effective length of database: 331
Effective search space:   110554
Effective search space used:   110554
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_015738684.1 ADEG_RS03370 (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.1885.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-123  397.4   0.0   3.6e-123  397.1   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015738684.1  ADEG_RS03370 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738684.1  ADEG_RS03370 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.1   0.0  3.6e-123  3.6e-123       1     341 [.      13     356 ..      13     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: 397.1 bits;  conditional E-value: 3.6e-123
                                 TIGR01357   1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 
                                               y+++vgegll+++ e +++    ++l+vi++++v+ l++e l+e l+++g++vl++ +pdgee+K+l+t
  lcl|NCBI__GCF_000024605.1:WP_015738684.1  13 YPIYVGEGLLARVGELTRQhlPGRRLMVISNSTVTGLYGEVLKESLEAAGWKVLWAEMPDGEEHKNLAT 81 
                                               689*********999999864449********************************************* PP

                                 TIGR01357  68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136
                                               v++l+d  +e +ler ++++a+GGGvvgD+aGFvAat++RG++  qvPTtlla+vD+svGGK+g+n+p+
  lcl|NCBI__GCF_000024605.1:WP_015738684.1  82 VSRLYDLAVEGELERGDAILAFGGGVVGDVAGFVAATFMRGVAWGQVPTTLLAQVDASVGGKVGVNHPQ 150
                                               ********************************************************************* PP

                                 TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205
                                               gkNliGaf+qP++V+ d+++l++lp+re+++GmaEv+K+g+i  a++f++le+n ++ll+la  eal++
  lcl|NCBI__GCF_000024605.1:WP_015738684.1 151 GKNLIGAFHQPRLVVADVDTLRSLPRREIASGMAEVVKYGVIRSASFFAWLEENVEALLSLAP-EALTH 218
                                               ********************************************************9998766.***** PP

                                 TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgl.l 272
                                               +++ s+++KaevV++DekesglRa+LNfGHt+gHa+Ea+++y  + HGeaVaiGmvv+ +l+++lgl +
  lcl|NCBI__GCF_000024605.1:WP_015738684.1 219 AVATSCRIKAEVVAADEKESGLRAILNFGHTVGHALEAMTDYVrFAHGEAVAIGMVVASRLARRLGLgF 287
                                               ******************************************99*********************9735 PP

                                 TIGR01357 273 kaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341
                                                ae+ +rl++ll+++glpt+l++ ++  ell ++++DKK +++k++++l+++iG++++ +ev++e lle
  lcl|NCBI__GCF_000024605.1:WP_015738684.1 288 TAEEERRLANLLEAIGLPTSLPPGTDPRELLLFMQRDKKVKEGKLTFILPRHIGEVEIVREVPQEILLE 356
                                               69999******************************************************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (360 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: 7.20
//
[ok]

This GapMind analysis is from Apr 10 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