GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Pseudomonas fluorescens FW300-N1B4

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate Pf1N1B4_1906 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906
          Length = 273

 Score =  442 bits (1138), Expect = e-129
 Identities = 216/272 (79%), Positives = 247/272 (90%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MD+YVVFGNPIGHSKSPLIHRLFAEQTGQ L+Y+TLLAPLD+FS CA+ FF++G G NVT
Sbjct: 1   MDRYVVFGNPIGHSKSPLIHRLFAEQTGQKLDYSTLLAPLDDFSGCAQAFFREGRGANVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKE+A+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG  LAGK
Sbjct: 61  VPFKEDAYRLANSLTKRAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGFSLAGK 120

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RIL+LGAGGAVRG LEP+LA +P S++IANRTVEKAE LA  F +LGPV ASGF WLQEP
Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASVIIANRTVEKAELLAELFADLGPVSASGFDWLQEP 180

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VD+IINATSASL+G++PPIA SL+E G+TVCYDMMYGK+PT FC+WA++ GAA  +DGLG
Sbjct: 181 VDLIINATSASLSGDVPPIASSLIEPGKTVCYDMMYGKDPTSFCRWASEHGAAVAMDGLG 240

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272
           MLAEQAAEAF++WRGVRPDTAPVLAELRRQLA
Sbjct: 241 MLAEQAAEAFYLWRGVRPDTAPVLAELRRQLA 272


Lambda     K      H
   0.319    0.137    0.405 

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: 331
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: 274
Length of database: 273
Length adjustment: 25
Effective length of query: 249
Effective length of database: 248
Effective search space:    61752
Effective search space used:    61752
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 Pf1N1B4_1906 (Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25))
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.27592.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
      9e-80  253.7   0.0      1e-79  253.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906  Shikimate 5-dehydrogenase I alph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906  Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0     1e-79     1e-79       3     269 ..       4     271 ..       2     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 1e-79
                                      TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKee 66 
                                                    + v+Gnpi hSksplih  +++q+g++l Y  + +++++++   ++++ +g +G+nvTvPfKe 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906   4 YVVFGNPIGHSKSPLIHRLFAEQTGQKLDYSTLLAPLDDFSGCAQAFFREG-RGANVTVPFKED 66 
                                                    78***********************************************99.8*********** PP

                                      TIGR00507  67 vlellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGa 128
                                                    +++l+  ++++a+ +gavNTl  l dg l+g+nTDg Glv +L     +  ++kr+l++GAGGa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906  67 AYRLANSLTKRAQRAGAVNTLSkLADGSLLGDNTDGAGLVRDLTVnAGFSLAGKRILLLGAGGA 130
                                                    *********************99*********************98888888************ PP

                                      TIGR00507 129 akavaleLlka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsagls 191
                                                     ++++ +Ll + + +viiaNRtvekae lae ++ lg + a    +  ++ vdliinatsa+ls
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 131 VRGALEPLLAEqPASVIIANRTVEKAELLAELFADLGPVSASGF-DWLQEPVDLIINATSASLS 193
                                                    ******98866489***********************9887665.455667************* PP

                                      TIGR00507 192 geideaevkaellkegk.lvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtg 253
                                                    g++  +++ ++l++ gk +++D++y +  t + ++a+++g +  +dGlgMl +Qaa +F lw+g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 194 GDV--PPIASSLIEPGKtVCYDMMYGKDPTSFCRWASEHGaAVAMDGLGMLAEQAAEAFYLWRG 255
                                                    ***..********98863789*******************66779******************* PP

                                      TIGR00507 254 vepdvekvfealkekl 269
                                                    v pd   v   l+++l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1906 256 VRPDTAPVLAELRRQL 271
                                                    *******999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (273 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: 00:00:00.00
# Mc/sec: 7.90
//
[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