Alignments for a candidate for aroD in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroD in Methanosarcina acetivorans C2A

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_011024466.1 MA_RS23970 3-dehydroquinase

Query= curated2:Q8PXE7
         (242 letters)



>NCBI__GCF_000007345.1:WP_011024466.1
          Length = 242

 Score =  360 bits (925), Expect = e-104
 Identities = 186/242 (76%), Positives = 209/242 (86%)

Query: 1   MTQIGSFDLEKKTAVVAVILEKPLENSKKAAEKGADILEIRLDLLGIRTPERAAEVIREI 60
           MTQIG FDLEKK AVVAVILEKPLE SKKAAEKGADILE+RLDLLGIR PE AA++IREI
Sbjct: 1   MTQIGPFDLEKKAAVVAVILEKPLETSKKAAEKGADILEVRLDLLGIRNPESAAKIIREI 60

Query: 61  KAETGIPIIVTSRSGAEGGKWDGKEEDRTGLLINLLSLKDGPDAIDIELSAGMKERNRVI 120
           K+ETG+P++VT+RS AEGGKW+GKE DRT LL+ LLSLKDGPDA+DIELSA  ++R++VI
Sbjct: 61  KSETGLPVLVTNRSVAEGGKWEGKEVDRTELLVALLSLKDGPDAVDIELSASREDRDKVI 120

Query: 121 KAAKDRETAVIVSSHDFLKTPPLQNMRTIIEEMFLAGADIAKLAVMPLSVGDTLNLLRVT 180
           KAAK     VI+SSHDF KTP  Q M   + EMFLA ADIAK+AVMP S+ D LNLL+VT
Sbjct: 121 KAAKAHGKTVIISSHDFSKTPSPQEMTATLAEMFLAEADIAKIAVMPGSMEDVLNLLKVT 180

Query: 181 LDFKDAGKSVCTIAMGSQGKHTRVVAPFYGSVLTYASIESNASAAPGQLPVDEVKKIMEM 240
           L+FK+ GK+VCTIAMG  GKHTRVVAP YGSVLTYASIESNA AAPGQLPVDEVKKIMEM
Sbjct: 181 LEFKNTGKTVCTIAMGKPGKHTRVVAPLYGSVLTYASIESNAVAAPGQLPVDEVKKIMEM 240

Query: 241 LK 242
           LK
Sbjct: 241 LK 242


Lambda     K      H
   0.315    0.133    0.360 

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: 251
Number of extensions: 2
Number of successful extensions: 1
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: 242
Length of database: 242
Length adjustment: 23
Effective length of query: 219
Effective length of database: 219
Effective search space:    47961
Effective search space used:    47961
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 (22.0 bits)
S2: 46 (22.3 bits)

Align candidate WP_011024466.1 MA_RS23970 (3-dehydroquinase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (EC 4.2.1.10))

# 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/TIGR01093.hmm
# target sequence database:        /tmp/gapView.27630.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01093  [M=229]
Accession:   TIGR01093
Description: aroD: 3-dehydroquinate dehydratase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-57  180.5   0.1    3.1e-57  180.3   0.1    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011024466.1  MA_RS23970 3-dehydroquinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011024466.1  MA_RS23970 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   0.1   3.1e-57   3.1e-57       7     228 ..      16     237 ..      12     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 3.1e-57
                                 TIGR01093   7 takdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkfk 75 
                                               +a  le+ le+ +k++e+gaDi+E+R+Dll   + e+   ++++++ +  + lp+++T R+  eGGk++
  lcl|NCBI__GCF_000007345.1:WP_011024466.1  16 VAVILEKPLETSKKAAEKGADILEVRLDLLGIRNPES-AAKIIREI-KSETGLPVLVTNRSVAEGGKWE 82 
                                               55567888999999999*************9999996.55555555.34599***************** PP

                                 TIGR01093  76 gdeeerleelkeaie.knlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverle 143
                                               g+e +r e+l +++  k ++d vDiEl+++ e  +++ik ak++++ +i+S+Hdf+ktps +e+ + l+
  lcl|NCBI__GCF_000007345.1:WP_011024466.1  83 GKEVDRTELLVALLSlKDGPDAVDIELSASREDRDKVIKAAKAHGKTVIISSHDFSKTPSPQEMTATLA 151
                                               ********99887753789************************************************** PP

                                 TIGR01093 144 kaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfg..s 210
                                               ++   +aDi+Kiavm+ s+eDvl+Ll++tl+ + ++ k + ++ Mg+ Gk +Rv++ + gsvlt++  +
  lcl|NCBI__GCF_000007345.1:WP_011024466.1 152 EMFLAEADIAKIAVMPGSMEDVLNLLKVTLEFK-NTGKTVCTIAMGKPGKHTRVVAPLYGSVLTYAsiE 219
                                               ********************************6.8899****************************444 PP

                                 TIGR01093 211 lgkasAPGQisvkelrel 228
                                               ++  +APGQ+ v+e++++
  lcl|NCBI__GCF_000007345.1:WP_011024466.1 220 SNAVAAPGQLPVDEVKKI 237
                                               45568**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (242 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: 7.26
//
[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