GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aroE in Azospirillum brasilense Sp245

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate AZOBR_RS01765 AZOBR_RS01765 shikimate 5-dehydrogenase

Query= curated2:Q2VYH4
         (276 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS01765 AZOBR_RS01765 shikimate
           5-dehydrogenase
          Length = 279

 Score =  367 bits (942), Expect = e-106
 Identities = 178/275 (64%), Positives = 212/275 (77%)

Query: 1   MSGKARLAGVLGWPVSHSRSPRLHGFWLEQMGIDGAYLPLAVAPEHLETVIRALPRMGFA 60
           +SGKA LAGV+GWP+ HSRSPRLHG+WLEQ GIDGAY+PLAV P+ +E  IRALP +GF 
Sbjct: 3   ISGKATLAGVMGWPIGHSRSPRLHGYWLEQYGIDGAYVPLAVPPDRIEQAIRALPALGFR 62

Query: 61  GANVTVPHKEAVMRLVDHLDPLARRIGAVNTLVVRQDGTLEGRNTDAYGFFENLRQGCPL 120
           G NVTVPHKEA  R VD LD  A+R+GAVNT+VV ++G+LEGRNTD +GF ENLR G P 
Sbjct: 63  GCNVTVPHKEAACRTVDRLDATAKRMGAVNTIVVGENGSLEGRNTDGFGFIENLRSGAPG 122

Query: 121 WEPTSGPAAVIGAGGAARAVVAALADAGVPEIRLANRSRERAATLAADLGGPVTVVDWAE 180
           W+   GPA VIGAGGAARAVVA+L D G P + L NR+R RA  LAAD+GG +   DW  
Sbjct: 123 WKAADGPALVIGAGGAARAVVASLLDEGAPRVWLVNRTRARADELAADIGGAIETADWVS 182

Query: 181 RAESLEGCALLVNTTTLGMTGQSSLDLDLAALPTTSVVNDIVYVPLVTDLLARATARGNP 240
           R   LEG AL+VNTTT GM GQ  L+L+L ALP ++VV DIVY PL+T LL  A ARGN 
Sbjct: 183 RETLLEGAALVVNTTTQGMAGQPPLELNLRALPGSAVVTDIVYTPLMTPLLTAAQARGNR 242

Query: 241 IVDGLGMLLHQAVPGFEAWFGQRPQVSDQLRAFVL 275
           +VDG+GMLLHQA PGF AWFG+ P+V++ L+A VL
Sbjct: 243 VVDGVGMLLHQARPGFAAWFGREPEVTEGLKAAVL 277


Lambda     K      H
   0.320    0.136    0.410 

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: 293
Number of extensions: 5
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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 AZOBR_RS01765 AZOBR_RS01765 (shikimate 5-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.28374.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.6e-71  225.4   0.0    4.4e-71  225.1   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS01765  AZOBR_RS01765 shikimate 5-dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS01765  AZOBR_RS01765 shikimate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   4.4e-71   4.4e-71       2     260 ..       9     270 ..       8     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 4.4e-71
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 
                                               l gv+G pi hS sp +h   l+q g+++ Y+ + v+++++e+a+ ++ alg++G+nvTvP+Ke++ + 
  lcl|FitnessBrowser__azobra:AZOBR_RS01765   9 LAGVMGWPIGHSRSPRLHGYWLEQYGIDGAYVPLAVPPDRIEQAIRALPALGFRGCNVTVPHKEAACRT 77 
                                               579****************************************************************** PP

                                 TIGR00507  71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek..lsklksekrvliiGAGGaakavaleL 136
                                               +D+++ +ak +gavNT++  e+g l+g nTDg G++ +L+     +  ++  +l+iGAGGaa+av+ +L
  lcl|FitnessBrowser__azobra:AZOBR_RS01765  78 VDRLDATAKRMGAVNTIVvGENGSLEGRNTDGFGFIENLRSgaPGWKAADGPALVIGAGGAARAVVASL 146
                                               *****************9789******************9975677788999***************** PP

                                 TIGR00507 137 lka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204
                                               l++   +v ++NRt ++a ela  +    e+  +   e  l+   l++n+t  g+ g+    e++   l
  lcl|FitnessBrowser__azobra:AZOBR_RS01765 147 LDEgAPRVWLVNRTRARADELAADIGGAIETADWVSRETLLEGAALVVNTTTQGMAGQP-PLELNLRAL 214
                                               **96679********************9999999999999****************998.78999999* PP

                                 TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260
                                                 +++v D+vy pl tpll  a+ +g +v+dG+gMl +Qa   F  w+g ep+v +
  lcl|FitnessBrowser__azobra:AZOBR_RS01765 215 PGSAVVTDIVYTPLMTPLLTAAQARGNRVVDGVGMLLHQARPGFAAWFGREPEVTE 270
                                               ****************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (279 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.38
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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