Alignments for a candidate for aroL in Methanothermobacter thermautotrophicus Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroL in Methanothermobacter thermautotrophicus Delta H

Align Shikimate kinase; SK; EC 2.7.1.71 (characterized)
to candidate WP_048061249.1 MTH_RS03785 shikimate kinase

Query= SwissProt::Q58835
         (282 letters)



>NCBI__GCF_000008645.1:WP_048061249.1
          Length = 286

 Score =  220 bits (560), Expect = 3e-62
 Identities = 121/281 (43%), Positives = 184/281 (65%), Gaps = 15/281 (5%)

Query: 10  SGTIINAIATGKGSAFGLDLKVYAKVKLIDDGKNKIEGKVLDNPNIKPNLIVRCVKNTLD 69
           S T+INAIATG+GSAFG+ L+V A+ +LID G   I  +  D      +L+  C +  ++
Sbjct: 10  SATVINAIATGRGSAFGIGLRVEAEAELIDSGVECISREGADT-----SLMELCTRMVIE 64

Query: 70  YFGLNYSAYVETKTEIPIKSGLSSSSATSNAVVLATFDALGEK-----IDDELILNLGIK 124
           ++G++    V T +++P+ SGLSSSSA SNA V+A    L ++     ++D  +LN+ + 
Sbjct: 65  HYGVDAGVRVVTSSDLPVASGLSSSSAASNATVMAVSSLLSDEFGLQPMEDFEMLNMAVD 124

Query: 125 SSFDEKLTVTGAYDDATASYYGGITITDNIERKILKRDKMRDDLNVLILIPN---LEKNV 181
           +S    ++VTGAYDDA+AS+YGG+T+TDN+ER+I+ R+ M +   VLI +P+   L    
Sbjct: 125 ASLQAGVSVTGAYDDASASFYGGLTVTDNMERRIILREPMENQ-KVLIYMPDRKSLTAQS 183

Query: 182 DVNRMKLIKDYVEIAFNEAINGNYFKALFLNGILYASALNFPTNIAIDALDAGAITAGLS 241
           DV RMKL+  +V++AF E ++G    AL LNGILY ++L F   IA+DAL+AGA+ AGLS
Sbjct: 184 DVPRMKLLAPWVDMAFREVLDGRVHSALTLNGILYCASLGFDPGIALDALEAGALAAGLS 243

Query: 242 GTGPSYIAMV-EDENVEKVKEKLNRYGKVILTKPNNDGASI 281
           GTGPS++A+  ED   + +    N  G V++T  +N+G  +
Sbjct: 244 GTGPSFVALTHEDSEADIIDAWENLEGDVLVTSVDNEGTRV 284


Lambda     K      H
   0.314    0.135    0.369 

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: 197
Number of extensions: 9
Number of successful extensions: 4
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: 282
Length of database: 286
Length adjustment: 26
Effective length of query: 256
Effective length of database: 260
Effective search space:    66560
Effective search space used:    66560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_048061249.1 MTH_RS03785 (shikimate kinase)
to HMM TIGR01920 (shikimate kinase (EC 2.7.1.71))

# 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/TIGR01920.hmm
# target sequence database:        /tmp/gapView.25443.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01920  [M=266]
Accession:   TIGR01920
Description: Shik_kin_archae: shikimate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.1e-82  262.4   0.8    2.4e-82  262.2   0.8    1.0  1  lcl|NCBI__GCF_000008645.1:WP_048061249.1  MTH_RS03785 shikimate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008645.1:WP_048061249.1  MTH_RS03785 shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.2   0.8   2.4e-82   2.4e-82       2     266 .]       8     275 ..       7     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.2 bits;  conditional E-value: 2.4e-82
                                 TIGR01920   2 sggitivnAlatGlGsAfgidLkveakvrlsdgeakvslkvreeeeldpelierilealieklgikegl 70 
                                                g+ t++nA+atG GsAfgi+L+vea+ +l+d  ++v+  +re   +d++l+e +   +ie++g+  g+
  lcl|NCBI__GCF_000008645.1:WP_048061249.1   8 PGSATVINAIATGRGSAFGIGLRVEAEAELID--SGVECISREG--ADTSLMELCTRMVIEHYGVDAGV 72 
                                               5899***************************9..7899999995..7********************** PP

                                 TIGR01920  71 eveveseiPagsGLksSsAlvnAlvlavlkakg.....eeiddieilrlgaelskeagvsvTGAfDDaa 134
                                                v + s++P++sGL+sSsA++nA+v+av  +++     + ++d+e+l++++ +s++agvsvTGA+DDa+
  lcl|NCBI__GCF_000008645.1:WP_048061249.1  73 RVVTSSDLPVASGLSSSSAASNATVMAVSSLLSdefglQPMEDFEMLNMAVDASLQAGVSVTGAYDDAS 141
                                               *******************************99444444589*************************** PP

                                 TIGR01920 135 asllggivltdNrkmkilkrdkleeetavvlvpkeeekeeevdlnelrkiskvveeavklAlkGeylkA 203
                                               as++gg+++tdN +++i+ r+++e++++++ +p +++++++ d+ +++  ++ v+ a++  l G    A
  lcl|NCBI__GCF_000008645.1:WP_048061249.1 142 ASFYGGLTVTDNMERRIILREPMENQKVLIYMPDRKSLTAQSDVPRMKLLAPWVDMAFREVLDGRVHSA 210
                                               ********************************************************************* PP

                                 TIGR01920 204 mvlngvlyataLgyplepaekalekGAavaglsGkGPsyvalteepe.eevaealeea.geVivv 266
                                               ++lng+ly++ Lg+++ +a +ale+GA++aglsG+GPs+valt+e+   ++  a+e+  g+V v+
  lcl|NCBI__GCF_000008645.1:WP_048061249.1 211 LTLNGILYCASLGFDPGIALDALEAGALAAGLSGTGPSFVALTHEDSeADIIDAWENLeGDVLVT 275
                                               *******************************************9998799************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (266 nodes)
Target sequences:                          1  (286 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: 00:00:00.01
# Mc/sec: 6.86
//
[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