Alignments for a candidate for aroE in Desulfovibrio vulgaris Hildenborough JW710

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Desulfovibrio vulgaris Hildenborough JW710

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate 209045 DVU0115 shikimate 5-dehydrogenase (TIGR)

Query= BRENDA::Q5SJF8
         (263 letters)



>FitnessBrowser__DvH:209045
          Length = 301

 Score =  174 bits (441), Expect = 2e-48
 Identities = 112/270 (41%), Positives = 146/270 (54%), Gaps = 15/270 (5%)

Query: 4   FAVLGHPVAHSLSPAMHAFALESLGLEGSYEAWDTPLEALPGRLKEVRRAFR-----GVN 58
           + ++GHP+ H+LSP +H +      L   Y AW  P    PGR      A R     G +
Sbjct: 37  YGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVP----PGRFASFMEAVRTLPVHGAS 92

Query: 59  LTLPLKEAALAHLDWVSPEAQRIGAVNTVLQVEGRLFGFNTDAPGFLEALKAGGIPLKGP 118
           +T+P KE AL   D V+  A+ +GAVNT+   +G + G NTD  GFL  L+A G+ +   
Sbjct: 93  VTIPHKEEALRLCDRVTDRARAVGAVNTLFLEDGVVCGENTDVTGFLAPLRARGVRI-DE 151

Query: 119 ALVLGAGGAGRAVAFALREAGL-EVWVWNRTPQRALALAEEFGLRAVPLEK--AREARLL 175
           ALVLGAGGA RAV   L E G+  V + NRT  +A+ LA  FG   VP ++  +  A L+
Sbjct: 152 ALVLGAGGAARAVLAGLVELGVRRVRISNRTHDKAMELAGAFGADVVPWDERGSAAAGLV 211

Query: 176 VNATRVGLEDP--SASPLPAELFPEEGAAVDLVYRPLWTRFLREAKAKGLKVQTGLPMLA 233
           VN T  G++      SPLP   F   G A DLVY PL TRFL +A+A G + Q GL M  
Sbjct: 212 VNTTPCGMQGARMGESPLPEGAFSGRGMAYDLVYNPLTTRFLADARAAGWETQDGLGMFV 271

Query: 234 WQGALAFRLWTGLLPDPSGMEEAARRALGV 263
            QG   FR+WTGL     G       ALG+
Sbjct: 272 EQGREQFRIWTGLDLPAEGARRLIAEALGL 301


Lambda     K      H
   0.320    0.137    0.417 

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: 235
Number of extensions: 10
Number of successful extensions: 3
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: 263
Length of database: 301
Length adjustment: 26
Effective length of query: 237
Effective length of database: 275
Effective search space:    65175
Effective search space used:    65175
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 209045 DVU0115 (shikimate 5-dehydrogenase (TIGR))
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.3611517.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
    3.4e-71  225.5   0.0    3.9e-71  225.3   0.0    1.0  1  FitnessBrowser__DvH:209045  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__DvH:209045  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   0.0   3.9e-71   3.9e-71       2     269 ..      36     299 ..      35     300 .. 0.95

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 3.9e-71
                   TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesakligav 84 
                                 l+g++G+p  h +spl+hn  ++   l  +Y+a +v++ ++ ++++++++l+++G++vT+P+Kee+l+l+D+++++a+++gav
  FitnessBrowser__DvH:209045  36 LYGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVPPGRFASFMEAVRTLPVHGASVTIPHKEEALRLCDRVTDRARAVGAV 118
                                 79********************************************************************************* PP

                   TIGR00507  85 NTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekaeelaerlqelgei 166
                                 NTl ledg + g+nTD+ G+++ L+    ++   ++l++GAGGaa+av+  L++    +v i NRt +ka ela ++ +    
  FitnessBrowser__DvH:209045 119 NTLFLEDGVVCGENTDVTGFLAPLRA-RGVR-IDEALVLGAGGAARAVLAGLVELgVRRVRISNRTHDKAMELAGAFGA---- 195
                                 *************************9.6666.679********************5578***************99998.... PP

                   TIGR00507 167 lalsleevelkkvdliinatsaglsgeid.eaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsF 248
                                   ++ +e       l++n+t+ g++g    e +++++ ++   +++Dlvynpl t +l+ a+  g +++dGlgM+v+Q+  +F
  FitnessBrowser__DvH:209045 196 DVVPWDERGSAAAGLVVNTTPCGMQGARMgESPLPEGAFSGRGMAYDLVYNPLTTRFLADARAAGWETQDGLGMFVEQGREQF 278
                                 556666888889**************9988***************************************************** PP

                   TIGR00507 249 elwtgvepdvekvfealkekl 269
                                 ++wtg   + e +++ ++e+l
  FitnessBrowser__DvH:209045 279 RIWTGLDLPAEGARRLIAEAL 299
                                 ******999999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (301 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: 18.08
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis