GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Enterococcus termitis LMG 8895

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_069665194.1 BCR25_RS19030 shikimate dehydrogenase

Query= SwissProt::Q8Y9N5
         (291 letters)



>NCBI__GCF_001730305.1:WP_069665194.1
          Length = 289

 Score =  280 bits (715), Expect = 4e-80
 Identities = 137/283 (48%), Positives = 190/283 (67%)

Query: 8   RITGHTELIGLIATPIRHSLSPTMHNEAFAKLGLDYVYLAFEVGDKELKDVVQGFRAMNL 67
           +ITG+T L  L ATPIRHS+SP +HN AF  LG+D VYLAFEVG   L+  +   R +++
Sbjct: 4   KITGNTRLAALFATPIRHSVSPIIHNTAFQALGIDAVYLAFEVGPDGLEQAIASIRNLDM 63

Query: 68  RGWNVSMPNKTNIHKYLDKLSPAAELVGAVNTVVNDDGVLTGHITDGTGYMRALKEAGHD 127
            G N+SMPNK     ++DKLS AA L+GA+NT+ N DG L GH TDG G+MR+L +    
Sbjct: 64  LGANLSMPNKLLAVNHMDKLSEAARLIGAINTITNQDGFLVGHNTDGIGFMRSLHDMNVT 123

Query: 128 IIGKKMTICGAGGAATAICIQAALDGVKEISIFNRKDDFYANAEKTVEKINSKTDCKAQL 187
           IIG KMT+ GAGGAA AI  QAALDGVKEI+++NR    Y  A+  +  I  +T+C+  L
Sbjct: 124 IIGHKMTVLGAGGAAAAIIAQAALDGVKEIAVYNRNSRSYEQAKAKLRYIAEQTNCRITL 183

Query: 188 FDIEDHEQLRKEIAESVIFTNATGVGMKPFEGETLLPSADMLRPELIVSDVVYKPTKTRL 247
            D+ D + L +++ ES +  N T VGMKP E  T +    ++ P+L+V D +Y P +T  
Sbjct: 184 NDLADEKALAQDVGESRLLLNTTSVGMKPLEKATPIQDFSIIGPDLVVYDAIYTPRETAF 243

Query: 248 LEIAEEQGCQTLNGLGMMLWQGAKAFEIWTHKEMPVDYIKEIL 290
           L+ A  +G  T NGLGM+L+QGA+AF++WT +E+P+  +K I+
Sbjct: 244 LKQARLRGALTANGLGMLLYQGAEAFKLWTGQELPISIVKPII 286


Lambda     K      H
   0.318    0.135    0.395 

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: 264
Number of extensions: 13
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: 291
Length of database: 289
Length adjustment: 26
Effective length of query: 265
Effective length of database: 263
Effective search space:    69695
Effective search space used:    69695
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_069665194.1 BCR25_RS19030 (shikimate dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

# 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/TIGR00507.hmm
# target sequence database:        /tmp/gapView.1272937.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00507  [M=270]
Accession:   TIGR00507
Description: aroE: shikimate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.7e-68  215.6   0.1    4.2e-68  215.4   0.1    1.0  1  NCBI__GCF_001730305.1:WP_069665194.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069665194.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.4   0.1   4.2e-68   4.2e-68       2     265 ..      11     286 ..      10     289 .] 0.85

  Alignments for each domain:
  == domain 1  score: 215.4 bits;  conditional E-value: 4.2e-68
                             TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDei 74 
                                           l +++  pi+hS+sp+ihn a++ lg++ +Ylafev ++ le+a+  i++l + G+n+ +P K  +++ +D++
  NCBI__GCF_001730305.1:WP_069665194.1  11 LAALFATPIRHSVSPIIHNTAFQALGIDAVYLAFEVGPDGLEQAIASIRNLDMLGANLSMPNKLLAVNHMDKL 83 
                                           5799********************************************************************* PP

                             TIGR00507  75 eesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka.dkeviia 146
                                           +e a+liga+NT++ +dg lvg+nTDgiG++ sL+ ++    ++++ ++GAGGaa a++ + +    ke+ + 
  NCBI__GCF_001730305.1:WP_069665194.1  84 SEAARLIGAINTITNQDGFLVGHNTDGIGFMRSLHDMNVTIIGHKMTVLGAGGAAAAIIAQAALDgVKEIAVY 156
                                           ************************************888888***************987765443899**** PP

                             TIGR00507 147 NR...tvekaeelaerlqe.lgeilalsleevelkk........vdliinatsaglsgeid.eaevkaellke 206
                                           NR   + e+a++ +  ++e +   + + l+++  +k          l++n+ts+g+++  +  ++ + +++  
  NCBI__GCF_001730305.1:WP_069665194.1 157 NRnsrSYEQAKAKLRYIAEqT--NCRITLNDLADEKalaqdvgeSRLLLNTTSVGMKPLEKaTPIQDFSIIGP 227
                                           *82224567777666676632..333333333333223223233569**********9877355556799999 PP

                             TIGR00507 207 gklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265
                                           + +v+D +y p et++lk a+ +g+ +++GlgMl +Q+a +F+lwtg+e +++ v+ ++
  NCBI__GCF_001730305.1:WP_069665194.1 228 DLVVYDAIYTPRETAFLKQARLRGALTANGLGMLLYQGAEAFKLWTGQELPISIVKPII 286
                                           *************************************************9998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (289 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: 15.25
//
[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:

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