Alignments for a candidate for aroE in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Cupriavidus basilensis 4G11

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate RR42_RS17645 RR42_RS17645 shikimate dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__Cup4G11:RR42_RS17645
          Length = 291

 Score =  276 bits (705), Expect = 5e-79
 Identities = 155/281 (55%), Positives = 192/281 (68%), Gaps = 14/281 (4%)

Query: 2   DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60
           D+YVV GNPI HS+SP IH  FA+QTG+ +EY  LLAPLD F    R FF  G  G NVT
Sbjct: 8   DRYVVIGNPIAHSRSPAIHAAFAQQTGEAVEYERLLAPLDGFVATVRAFFDGGGHGLNVT 67

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFK EA+ L + LTPRA  AGAVNT+  + DG + GDNTDG GL RD+ VN    L GK
Sbjct: 68  VPFKLEAYDLAERLTPRAESAGAVNTMW-IEDGVIHGDNTDGVGLTRDIEVNLDTLLEGK 126

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKA----EQLAREFDELG-PVVASGFA 175
           RIL+LGAGGA  G + P++A +P+ +V+ANRT ++A    E +A++ DE G  +   GF 
Sbjct: 127 RILLLGAGGAAMGAMLPLIACRPERIVVANRTPQRASDILENVAQQADEYGVELWGGGFD 186

Query: 176 WL-----QEPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKL 230
            L     ++  DV+INATS+SL GELPP+   L+  G  + YDMMYG EPT F ++A + 
Sbjct: 187 ALAGLTDEDACDVVINATSSSLQGELPPVPAELLGKG-VLAYDMMYGAEPTVFLKFAAQC 245

Query: 231 GAAKVLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271
           G A+  DGLGML EQAAEAF+ WRGVRP TAPVLA LR  L
Sbjct: 246 G-ARTSDGLGMLVEQAAEAFYNWRGVRPATAPVLATLRAAL 285


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: 280
Number of extensions: 14
Number of successful extensions: 6
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: 291
Length adjustment: 26
Effective length of query: 248
Effective length of database: 265
Effective search space:    65720
Effective search space used:    65720
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 RR42_RS17645 RR42_RS17645 (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.21755.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.9e-78  248.7   0.0    3.5e-78  248.5   0.0    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS17645  RR42_RS17645 shikimate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS17645  RR42_RS17645 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.5   0.0   3.5e-78   3.5e-78       3     269 ..      10     285 ..       8     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: 248.5 bits;  conditional E-value: 3.5e-78
                                 TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 
                                               + viGnpi+hS sp+ih a+++q+g ++eY ++ ++++ +  ++ +++  g +G+nvTvPfK e+++l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS17645  10 YVVIGNPIAHSRSPAIHAAFAQQTGEAVEYERLLAPLDGFVATVRAFFDGGGHGLNVTVPFKLEAYDLA 78 
                                               78******************************************************************* PP

                                 TIGR00507  72 DeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka 139
                                               ++++++a+ +gavNT+ +edg + g+nTDg+Gl+ ++e  l++l ++kr+l++GAGGaa +++l+L   
  lcl|FitnessBrowser__Cup4G11:RR42_RS17645  79 ERLTPRAESAGAVNTMWIEDGVIHGDNTDGVGLTRDIEVnLDTLLEGKRILLLGAGGAAMGAMLPLIAC 147
                                               **************************************99**************************998 PP

                                 TIGR00507 140 .dkeviiaNRtvekaeelaerlqe..........lgeilalsleevelkkvdliinatsaglsgeidea 197
                                                ++++++aNRt ++a +++e +++           g   al     +++  d++inats++l+ge+  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS17645 148 rPERIVVANRTPQRASDILENVAQqadeygvelwGGGFDALA-GLTDEDACDVVINATSSSLQGEL--P 213
                                               799*****************9999777744443212222222.3346667****************..* PP

                                 TIGR00507 198 evkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266
                                               +v+aell +g l++D++y    t++lk a + g++++dGlgMlv+Qaa +F  w+gv p    v  +l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS17645 214 PVPAELLGKGVLAYDMMYGAEPTVFLKFAAQCGARTSDGLGMLVEQAAEAFYNWRGVRPATAPVLATLR 282
                                               ************************************************************999999888 PP

                                 TIGR00507 267 ekl 269
                                               ++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS17645 283 AAL 285
                                               877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (291 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: 00:00:00.01
# Mc/sec: 6.18
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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