GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Pontibacter ramchanderi LP43

Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_101446022.1 BD749_RS15575 3-dehydroquinate synthase

Query= curated2:A6LEZ7
         (353 letters)



>NCBI__GCF_002846395.1:WP_101446022.1
          Length = 345

 Score =  243 bits (620), Expect = 5e-69
 Identities = 136/346 (39%), Positives = 204/346 (58%), Gaps = 6/346 (1%)

Query: 4   QKVVICKDLKSELQDFLSSLKYDKLFILMDTNTKEKCFPLVEDIPAFQKAPILVMEAGDM 63
           + + I +D+  +L+  L +L + K+ +L+D NT   C+P V+  P      I+ +++G+ 
Sbjct: 3   ENIYIGRDVLPQLKAALQNLAFSKVAVLVDENTLHHCYPQVK--PYLPAHDIIQIQSGEA 60

Query: 64  NKGFVSLAQIWTALSNEGASRNSLLVNLGGGMITDMGGFAGATFKRGIRTINIPTTLMAS 123
           +K   +   IW  +++    R S+LVNLGGG+I DMGGF  ATFKRG+  + +PTTL+A 
Sbjct: 61  HKTLQTCEYIWQRMTDLNLDRWSVLVNLGGGVIGDMGGFCAATFKRGLYFVQVPTTLLAQ 120

Query: 124 VDAAVGGKTGINFNGLKNEVGSFYPPLCVFIDCDFLRTLDRDNILSGYAEMIKHGLISSM 183
           VDA+VGGKTGI+F+GLKN +G +  P  V ID  FL TL +  + SGYAE+IKH LI+  
Sbjct: 121 VDASVGGKTGIDFHGLKNHIGVYKEPHAVLIDPTFLGTLPQRQVKSGYAEIIKHWLIADA 180

Query: 184 ENYASVMLFDIDTMNYSYLNSLVGQSVAVKERIVEEDPKEQGIRKALNFGHTIGHAFES- 242
             +       + T ++   ++L+  SV +K  +VE DP E G RK LNFGHT+GHA ES 
Sbjct: 181 AAFEEQRHIGLLTEDW---DTLIRHSVGIKAAVVEADPLEGGYRKVLNFGHTVGHAVESY 237

Query: 243 LSFLKMRPILHGHAVAAGIVSELYLSHKLCGFPMEKLSQVVYYIKEYYPALFFDCTDYDT 302
           L     R +LHG A+A G++ E YLS K       +L Q+  ++   Y  +     D   
Sbjct: 238 LMDQPGRALLHGEAIAVGMLCEAYLSMKKDLLSKRELEQIETFLVSVYEKVKLTEDDIQA 297

Query: 303 LYELMTHDKKNEGGIINFTLLKNVGDVRINQSVTKEKILESLDFYR 348
           +  L+  DKKN    IN TLL+ +G    +Q +T  +I ++L +Y+
Sbjct: 298 ITRLVLQDKKNTHSTINCTLLQGIGKAVWDQPITLTEIQDALRYYQ 343


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: 295
Number of extensions: 10
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: 345
Length adjustment: 29
Effective length of query: 324
Effective length of database: 316
Effective search space:   102384
Effective search space used:   102384
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_101446022.1 BD749_RS15575 (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.33919.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-103  330.8   0.0     6e-103  330.6   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101446022.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101446022.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.6   0.0    6e-103    6e-103       2     338 ..       4     334 ..       3     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 330.6 bits;  conditional E-value: 6e-103
                             TIGR01357   2 kvkvgegllkklveelaeka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklld 73 
                                           ++++g+++l +l ++l++ a sk+ v++de++ +++  +++  l +    ++++ +++ge +K+l+t++ +++
  NCBI__GCF_002846395.1:WP_101446022.1   4 NIYIGRDVLPQLKAALQNLAfSKVAVLVDENTLHHCYPQVKPYLPA----HDIIQIQSGEAHKTLQTCEYIWQ 72 
                                           699**************9666***************9999999865....99********************* PP

                             TIGR01357  74 qlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyq 146
                                           ++ + +l+r svlv++GGGv+gD++GF Aat++RG+ +vqvPTtlla+vD+svGGKtgi++++ kN iG + +
  NCBI__GCF_002846395.1:WP_101446022.1  73 RMTDLNLDRWSVLVNLGGGVIGDMGGFCAATFKRGLYFVQVPTTLLAQVDASVGGKTGIDFHGLKNHIGVYKE 145
                                           ************************************************************************* PP

                             TIGR01357 147 PkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVe 219
                                           P+aVlid+++l tlp+r++++G+aE+iKh liada+ fee +++   l+     e +++li++s+ +Ka vVe
  NCBI__GCF_002846395.1:WP_101446022.1 146 PHAVLIDPTFLGTLPQRQVKSGYAEIIKHWLIADAAAFEEQRHIGL-LT-----EDWDTLIRHSVGIKAAVVE 212
                                           **************************************99887553.33.....679**************** PP

                             TIGR01357 220 eDekesglRalLNfGHtlgHaiEallkyk....lsHGeaVaiGmvveaklseklgllkaellerlvallkklg 288
                                           +D+ e g R++LNfGHt+gHa+E+ l  +    l HGea+a+Gm +ea+ls k+ ll++++le+++++l +++
  NCBI__GCF_002846395.1:WP_101446022.1 213 ADPLEGGYRKVLNFGHTVGHAVESYLMDQpgraLLHGEAIAVGMLCEAYLSMKKDLLSKRELEQIETFLVSVY 285
                                           ************************988777899**************************************** PP

                             TIGR01357 289 lptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteee 338
                                            ++kl++  +++++++ +l+DKKn +s+i+  ll+ iGka+ ++ +t +e
  NCBI__GCF_002846395.1:WP_101446022.1 286 EKVKLTE-DDIQAITRLVLQDKKNTHSTINCTLLQGIGKAVWDQPITLTE 334
                                           ******7.9*******************************9887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (345 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: 16.27
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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:

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:

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:

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:

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