Alignments for a candidate for aroE in Sulfurivirga caldicuralii DSM 17737

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Sulfurivirga caldicuralii DSM 17737

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_074200494.1 BUQ81_RS00770 shikimate dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>NCBI__GCF_900141795.1:WP_074200494.1
          Length = 278

 Score =  257 bits (656), Expect = 2e-73
 Identities = 152/277 (54%), Positives = 183/277 (66%), Gaps = 7/277 (2%)

Query: 2   DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDE--FSDCARGFFKQGSGG-N 58
           D+Y V G PI HSKSPLIHRLFAEQTG+DL Y  +L   DE  F+   R     G  G N
Sbjct: 3   DKYAVVGYPIAHSKSPLIHRLFAEQTGEDLVYEAILIDADEKPFAAAVRELMALGYRGLN 62

Query: 59  VTVPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELA 118
           VTVP+K +AF   D+LT RA  A AVNTL+   +G L GDNTDG GLV+D+   AGV L 
Sbjct: 63  VTVPYKLDAFEFADTLTDRADIAQAVNTLTFTDEGVL-GDNTDGVGLVQDIEELAGVSLR 121

Query: 119 GKRILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ 178
           GK +LILGAGGAV+GVL P+LA  P S+ IANRT  +AE LAR F +      +  A   
Sbjct: 122 GKSVLILGAGGAVQGVLHPLLAADPNSIFIANRTAGRAEALARRFADARVSGGTFEAIPD 181

Query: 179 EPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGA-AKVLD 237
            P DVIIN T+ASL G+LPPI  +++  G ++ YDMMY  EPT F +WA++      V D
Sbjct: 182 TPFDVIINGTAASLEGKLPPIPTAVI-GGNSLVYDMMYAAEPTVFLRWASETQPNCTVRD 240

Query: 238 GLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQLARG 274
           GLGML  QAAEAF  WRGVRP +APVL E  R++ RG
Sbjct: 241 GLGMLVCQAAEAFASWRGVRPQSAPVL-EAVRKIIRG 276


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: 244
Number of extensions: 13
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: 278
Length adjustment: 25
Effective length of query: 249
Effective length of database: 253
Effective search space:    62997
Effective search space used:    62997
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 WP_074200494.1 BUQ81_RS00770 (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.25237.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-78  248.4   0.0    4.1e-78  248.2   0.0    1.0  1  lcl|NCBI__GCF_900141795.1:WP_074200494.1  BUQ81_RS00770 shikimate dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900141795.1:WP_074200494.1  BUQ81_RS00770 shikimate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.2   0.0   4.1e-78   4.1e-78       2     268 ..       4     273 ..       3     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 248.2 bits;  conditional E-value: 4.1e-78
                                 TIGR00507   2 llgviGnpikhSksplihnaalkqlgleleYlafeveiee..lekalsgikalglkGvnvTvPfKeevl 68 
                                                ++v+G+pi+hSksplih  +++q+g +l+Y a+ ++ +e  +  a+ ++ alg +G+nvTvP+K  ++
  lcl|NCBI__GCF_900141795.1:WP_074200494.1   4 KYAVVGYPIAHSKSPLIHRLFAEQTGEDLVYEAILIDADEkpFAAAVRELMALGYRGLNVTVPYKLDAF 72 
                                               59*******************************9999888789************************** PP

                                 TIGR00507  69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLekls..klksekrvliiGAGGaakavale 135
                                               e++D ++++a  ++avNTl+  d+ ++g+nTDg+Glv+++e+l    l+ +k+vli+GAGGa ++v+ +
  lcl|NCBI__GCF_900141795.1:WP_074200494.1  73 EFADTLTDRADIAQAVNTLTFTDEGVLGDNTDGVGLVQDIEELAgvSLR-GKSVLILGAGGAVQGVLHP 140
                                               ******************************************6511445.9****************** PP

                                 TIGR00507 136 Llka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkael 203
                                               Ll a ++++ iaNRt  +ae+la r++    +     e ++   +d+iin t+a+l+g++  +++++ +
  lcl|NCBI__GCF_900141795.1:WP_074200494.1 141 LLAAdPNSIFIANRTAGRAEALARRFAD-ARVSGGTFEAIPDTPFDVIINGTAASLEGKL--PPIPTAV 206
                                               **997899*******************9.56666677899999*****************..******* PP

                                 TIGR00507 204 lkegklvvDlvynpletpllkeakkkg..tkvidGlgMlvaQaalsFelwtgvepdvekvfealkek 268
                                               +  ++lv+D++y+   t++l++a++ +  + v dGlgMlv Qaa +F  w+gv p+   v ea+++ 
  lcl|NCBI__GCF_900141795.1:WP_074200494.1 207 IGGNSLVYDMMYAAEPTVFLRWASETQpnCTVRDGLGMLVCQAAEAFASWRGVRPQSAPVLEAVRKI 273
                                               ***********************99876799***************************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (278 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: 8.30
//
[ok]

This GapMind analysis is from Apr 10 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:

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