GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Magnetospirillum magneticum AMB-1

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_043745705.1 AMB_RS23010 shikimate dehydrogenase

Query= reanno::Caulo:CCNA_00003
         (285 letters)



>NCBI__GCF_000009985.1:WP_043745705.1
          Length = 278

 Score =  199 bits (506), Expect = 6e-56
 Identities = 111/275 (40%), Positives = 146/275 (53%)

Query: 5   ITGAAIVGGVCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVR 64
           ++G A + GV G P+ HS SP +H  W+   G+D AY+P A A +  ET +  L      
Sbjct: 3   VSGKARLAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFA 62

Query: 65  GLNVTIPFKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPG 124
           G NVT+P KE  + + D    LAR  GA N LV  +DG++   NTD  G    +    P 
Sbjct: 63  GANVTVPHKEAVMRLVDHLDPLARRIGAVNTLVVRQDGTLEGRNTDAYGFFENLRQGCPL 122

Query: 125 FDVTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDA 184
           ++ T+ P  ++GAGGAAR  VAAL  AG P I + NR+  RA  LA   G  V       
Sbjct: 123 WEPTSGPAAVIGAGGAARAVVAALADAGVPEIRLANRSRERAATLAADLGGPVTVVDWAE 182

Query: 185 LPALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRR 244
               L    L++N T+LG+ G +    DL   P T+VV D+VY PL T+ L RA A G  
Sbjct: 183 RAESLEGCALLVNTTTLGMTGQSSLDLDLAALPTTSVVNDIVYVPLVTDLLARATARGNP 242

Query: 245 TVDGLEMLLRQAIPTFETIYGQAPSPKIDVRVLAL 279
            VDGL MLL QA+P FE  +GQ P     +R   L
Sbjct: 243 IVDGLGMLLHQAVPGFEAWFGQRPQVSDQLRAFVL 277


Lambda     K      H
   0.319    0.136    0.390 

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: 203
Number of extensions: 9
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: 285
Length of database: 278
Length adjustment: 26
Effective length of query: 259
Effective length of database: 252
Effective search space:    65268
Effective search space used:    65268
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: 47 (22.7 bits)

Align candidate WP_043745705.1 AMB_RS23010 (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.28340.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.6e-69  218.5   0.0    5.5e-69  218.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043745705.1  AMB_RS23010 shikimate dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043745705.1  AMB_RS23010 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.3   0.0   5.5e-69   5.5e-69       2     260 ..       9     270 ..       8     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 5.5e-69
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               l gv+G p+ hS sp +h   l+q+g+++ Yl + v +e+le ++ ++   g+ G+nvTvP+Ke+v++l
  lcl|NCBI__GCF_000009985.1:WP_043745705.1   9 LAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFAGANVTVPHKEAVMRL 77 
                                               579****************************************************************** PP

                                 TIGR00507  71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek...lsklksekrvliiGAGGaakavale 135
                                               +D++++ a+ igavNTl+ ++dg l+g nTD++G++ +L++   l ++     +++iGAGGaa+av+ +
  lcl|NCBI__GCF_000009985.1:WP_043745705.1  78 VDHLDPLARRIGAVNTLVvRQDGTLEGRNTDAYGFFENLRQgcpLWEPT-SGPAAVIGAGGAARAVVAA 145
                                               *****************988999******************74333333.56799************** PP

                                 TIGR00507 136 Llka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkael 203
                                               L++a   e+ +aNR+ e+a  la  l    +++ + +    l+   l++n+t +g++g+     ++   
  lcl|NCBI__GCF_000009985.1:WP_043745705.1 146 LADAgVPEIRLANRSRERAATLAADLGGPVTVVDWAERAESLEGCALLVNTTTLGMTGQS-SLDLDLAA 213
                                               ****5569******************99999*****99*********************9.89999999 PP

                                 TIGR00507 204 lkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260
                                               l + ++v D+vy pl t ll+ a  +g +++dGlgMl +Qa+  Fe w+g+ p+v+ 
  lcl|NCBI__GCF_000009985.1:WP_043745705.1 214 LPTTSVVNDIVYVPLVTDLLARATARGNPIVDGLGMLLHQAVPGFEAWFGQRPQVSD 270
                                               9****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (278 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: 6.83
//
[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:

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