Alignments for a candidate for aroD in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroD in Clostridium kluyveri DSM 555

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type I DHQase; Type I dehydroquinase; DHQ1; EC 4.2.1.10 (characterized)
to candidate WP_012101381.1 CKL_RS04955 3-dehydroquinase

Query= SwissProt::Q186A6
         (255 letters)



>NCBI__GCF_000016505.1:WP_012101381.1
          Length = 255

 Score =  268 bits (686), Expect = 6e-77
 Identities = 130/247 (52%), Positives = 188/247 (76%), Gaps = 1/247 (0%)

Query: 5   VQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKE 64
           V+++++ +GEG PKI VP++G N+++I++E   +K   LDI+EWR+D+++ VE +++VK+
Sbjct: 5   VKIRDVKLGEGIPKIAVPLVGSNEEEIMEEIAGVKTTKLDIVEWRIDYYKYVEEVEKVKK 64

Query: 65  VLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMG-DE 123
           +L ++R  +++IP+L TFR+  EGG++ IS +YY  LNK I+ TG  D+ID+ELF   DE
Sbjct: 65  LLQKMRKNLNNIPILVTFRTAKEGGKREISLEYYIELNKAIAATGNTDMIDIELFAAEDE 124

Query: 124 VIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVL 183
            + ++V   H+  +KVI+SNHDF+KTP K+E++SR+CRMQ+LGAD+ KIAVMP + KDVL
Sbjct: 125 AVKKIVEELHEYNIKVIMSNHDFHKTPHKDELISRMCRMQQLGADIAKIAVMPCSTKDVL 184

Query: 184 VLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKEL 243
            LL AT EM   + D PIITMSM  +GVI+RL GE FGSALTFG+AK+ SAPGQ+   EL
Sbjct: 185 ELLSATCEMKCKHNDTPIITMSMGTLGVITRLAGETFGSALTFGSAKAASAPGQLEVNEL 244

Query: 244 NSVLNLL 250
             VL L+
Sbjct: 245 YKVLKLI 251


Lambda     K      H
   0.319    0.138    0.386 

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: 224
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_012101381.1 CKL_RS04955 (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.26274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.9e-79  252.4   1.0    3.3e-79  252.2   1.0    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012101381.1  CKL_RS04955 3-dehydroquinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012101381.1  CKL_RS04955 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.2   1.0   3.3e-79   3.3e-79       1     228 [.      18     247 ..      18     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.2 bits;  conditional E-value: 3.3e-79
                                 TIGR01093   1 kilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqk 69 
                                               ki+vpl+  + ee++ee+  +k++  DivE+R+D++k v++ ++v+++ +++++ l+++p+++T+Rt+k
  lcl|NCBI__GCF_000016505.1:WP_012101381.1  18 KIAVPLVGSNEEEIMEEIAGVKTTKLDIVEWRIDYYKYVEEVEKVKKLLQKMRKNLNNIPILVTFRTAK 86 
                                               699****************************************************************** PP

                                 TIGR01093  70 eGGkfkgdeeerleelkeaieknlvdlvDiElkle.eeavkelikeakkaktkiilSnHdfektpskee 137
                                               eGGk + + e+++e++k+++  ++ d++DiEl+++ +eavk++++e ++ ++k+i+SnHdf+ktp k+e
  lcl|NCBI__GCF_000016505.1:WP_012101381.1  87 EGGKREISLEYYIELNKAIAATGNTDMIDIELFAAeDEAVKKIVEELHEYNIKVIMSNHDFHKTPHKDE 155
                                               ********************************9751678999*************************** PP

                                 TIGR01093 138 lverlekaqsldaDivKiavmaksieDvltLleitlkveeek.dkplialsMgekGkisRvlgavlgsv 205
                                               l++r+ ++q+l+aDi+Kiavm+ s++Dvl+Ll++t +++ ++ d p+i++sMg  G i+R++g+ +gs+
  lcl|NCBI__GCF_000016505.1:WP_012101381.1 156 LISRMCRMQQLGADIAKIAVMPCSTKDVLELLSATCEMKCKHnDTPIITMSMGTLGVITRLAGETFGSA 224
                                               **************************************98888************************** PP

                                 TIGR01093 206 ltfgslgkasAPGQisvkelrel 228
                                               ltfgs++ asAPGQ++v+el ++
  lcl|NCBI__GCF_000016505.1:WP_012101381.1 225 LTFGSAKAASAPGQLEVNELYKV 247
                                               *******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (229 nodes)
Target sequences:                          1  (255 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.56
//
[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