Aligments for a candidate for aroE in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Aligments for a candidate for aroE in Desulfovibrio vulgaris Miyazaki F

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate 8501228 DvMF_1962 shikimate 5-dehydrogenase (RefSeq)

Query= curated2:Q30VD9
         (279 letters)



>lcl|FitnessBrowser__Miya:8501228 DvMF_1962 shikimate
           5-dehydrogenase (RefSeq)
          Length = 315

 Score =  290 bits (743), Expect = 2e-83
 Identities = 158/292 (54%), Positives = 191/292 (65%), Gaps = 17/292 (5%)

Query: 4   PRIPRQLYGIIGYPLGHSMSPLLHNWGFELLGEQAAYMAFPVAPEKLAEFICCARMLPVS 63
           P +PR+LYGIIG+PLGH+MSPLLHNWGF LL   A YMA+P+ P ++ +FI   R LP+ 
Sbjct: 5   PFLPRELYGIIGHPLGHTMSPLLHNWGFSLLDVPAVYMAWPLEPGRVGDFITAVRTLPIR 64

Query: 64  GLSVTIPHKQAVMPLLDAVTPRAQAAGAVNTLFYDDGKLTGDNTDVYGFLHPL---DSCG 120
           G SVTIPHKQAV+PLLD V+ RA+A GAVNTL++ DG+L G+NTDV GFL PL    + G
Sbjct: 65  GASVTIPHKQAVLPLLDGVSDRARAVGAVNTLYWRDGQLLGENTDVTGFLAPLRQRAAAG 124

Query: 121 TAHAAALVLGAGGAANAVLAALTARGMCN------VTVTNRNGDRARILAERFGVRCVAW 174
                ALVLG GGAA AVLA L   G         V VT RN ++A  LA  FG   V W
Sbjct: 125 WRCERALVLGNGGAARAVLAGLRELGPAGDGVVRAVGVTGRNAEKAAPLAAEFGAEVVDW 184

Query: 175 EERHAVDADLVVNTTPLGMAGDRQAQTPLDPAFFSSRPA--------GLAYDLIYNPAQT 226
           + R    ADLVVNTTP+GM+G+RQ  T      F+++          GLAYDL+YNP +T
Sbjct: 185 DARVHWGADLVVNTTPMGMSGERQGDTAFPEQGFAAQGVAAGGDGRRGLAYDLVYNPLRT 244

Query: 227 FFLASAQAAGWRVLNGLDMFVAQGAEQFRIWRGRELPFAQARALIADALASG 278
            FL+ A  AGW   +GL MFV QG EQFR+W G ELP   AR L+A AL  G
Sbjct: 245 RFLSEAADAGWDTQDGLGMFVEQGREQFRLWTGLELPAEGARTLVAVALGLG 296


Lambda     K      H
   0.324    0.137    0.427 

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: 304
Number of extensions: 13
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: 279
Length of database: 315
Length adjustment: 26
Effective length of query: 253
Effective length of database: 289
Effective search space:    73117
Effective search space used:    73117
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate 8501228 DvMF_1962 (shikimate 5-dehydrogenase (RefSeq))
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.31134.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    9.8e-64  201.1   0.0    1.3e-63  200.6   0.0    1.2  1  lcl|FitnessBrowser__Miya:8501228  DvMF_1962 shikimate 5-dehydrogen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501228  DvMF_1962 shikimate 5-dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.0   1.3e-63   1.3e-63       2     266 ..      11     290 ..      10     294 .. 0.86

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 1.3e-63
                         TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeieesa 78 
                                       l+g+iG+p  h +spl+hn  ++ l++  +Y+a ++e+ ++ ++++++++l+++G++vT+P+K++vl+llD ++++a
  lcl|FitnessBrowser__Miya:8501228  11 LYGIIGHPLGHTMSPLLHNWGFSLLDVPAVYMAWPLEPGRVGDFITAVRTLPIRGASVTIPHKQAVLPLLDGVSDRA 87 
                                       89*************************************************************************** PP

                         TIGR00507  79 kligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlkad.......keviiaN 147
                                       +++gavNTl  +dg+l+g+nTD+ G+++ L++        +r+l++G GGaa+av+  L + +        +v ++ 
  lcl|FitnessBrowser__Miya:8501228  88 RAVGAVNTLYWRDGQLLGENTDVTGFLAPLRQrAAAGWRCERALVLGNGGAARAVLAGLRELGpagdgvvRAVGVTG 164
                                       ********************************655545589****************99987522233334677889 PP

                         TIGR00507 148 Rtvekaeelaerlqelgeilalsleevelkk.vdliinatsaglsgeid.eaevkaellkegk..........lvvD 212
                                       R  eka  la ++ +  e++ ++    + +   dl++n+t++g+sge + +++ +++ ++++           l++D
  lcl|FitnessBrowser__Miya:8501228 165 RNAEKAAPLAAEFGA--EVVDWD---ARVHWgADLVVNTTPMGMSGERQgDTAFPEQGFAAQGvaaggdgrrgLAYD 236
                                       998888888888877..666676...3334349**************9999999888776543111122222378** PP

                         TIGR00507 213 lvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266
                                       lvynpl t +l+ea + g  ++dGlgM+v+Q+  +F+lwtg e + e ++  ++
  lcl|FitnessBrowser__Miya:8501228 237 LVYNPLRTRFLSEAADAGWDTQDGLGMFVEQGREQFRLWTGLELPAEGARTLVA 290
                                       ******************************************998888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (315 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: 00:00:00.00
# Mc/sec: 9.99
//
[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:

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, 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

GapMind for Amino acid biosynthesis