Alignments for a candidate for dch in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for dch in Magnetospirillum magneticum AMB-1

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_011384541.1 AMB_RS10825 cyclohexa-1,5-dienecarbonyl-CoA hydratase

Query= BRENDA::O87873
         (258 letters)



>NCBI__GCF_000009985.1:WP_011384541.1
          Length = 259

 Score =  337 bits (865), Expect = 1e-97
 Identities = 174/254 (68%), Positives = 204/254 (80%)

Query: 5   SSPLKVWLERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHF 64
           S+ LKVW +R+G LLRLRL+RPKANIVDA MIAA+  ALG+  +  ALRAVL+D EGPHF
Sbjct: 6   SNCLKVWKDREGKLLRLRLSRPKANIVDAEMIAALSAALGDAHEDSALRAVLIDHEGPHF 65

Query: 65  SFGASVDEHMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAA 124
           SFGASV EHMPDQCA ML SLH LV  M+D P+PILVA+RGQCLGGGLEVA AG+++F +
Sbjct: 66  SFGASVAEHMPDQCAAMLASLHKLVIAMVDFPLPILVAVRGQCLGGGLEVALAGHMMFVS 125

Query: 125 PDAKFGQPEIRLGVFAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDP 184
           PDAK GQPEI LGVFAPAASCLLP R+ +  AEDLL+SGRSIDGAE  R+G+ + + +DP
Sbjct: 126 PDAKLGQPEIVLGVFAPAASCLLPERMPRVAAEDLLYSGRSIDGAEAARLGIANAVVDDP 185

Query: 185 EAAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHDAVEGL 244
           E AAL WFD   A+ SA+SLRFAV+AAR     R+K K+  VEALYL  LMA+HDAVEGL
Sbjct: 186 ENAALAWFDNGPAKHSAASLRFAVKAARLGMNERVKAKIAEVEALYLNGLMATHDAVEGL 245

Query: 245 KAFLEKRSANWENR 258
            AFLEKR A WE+R
Sbjct: 246 NAFLEKRPALWEDR 259


Lambda     K      H
   0.321    0.135    0.402 

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: 277
Number of extensions: 13
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_011384541.1 AMB_RS10825 (cyclohexa-1,5-dienecarbonyl-CoA hydratase)
to HMM TIGR03189 (cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100))

# 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.carbon/TIGR03189.hmm
# target sequence database:        /tmp/gapView.6819.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03189  [M=251]
Accession:   TIGR03189
Description: dienoyl_CoA_hyt: cyclohexa-1,5-dienecarbonyl-CoA hydratase
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-157  507.6   5.9   2.9e-157  507.5   5.9    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384541.1  AMB_RS10825 cyclohexa-1,5-dienec


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384541.1  AMB_RS10825 cyclohexa-1,5-dienecarbonyl-CoA hydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.5   5.9  2.9e-157  2.9e-157       1     251 []       9     259 .]       9     259 .] 1.00

  Alignments for each domain:
  == domain 1  score: 507.5 bits;  conditional E-value: 2.9e-157
                                 TIGR03189   1 lkvwlerdgkllrlrlarpkanivdaamiaalraalgealeaaalravlldaegphfsfgasveehmpd 69 
                                               lkvw++r+gkllrlrl+rpkanivda+miaal+aalg+a+e++alravl+d+egphfsfgasv+ehmpd
  lcl|NCBI__GCF_000009985.1:WP_011384541.1   9 LKVWKDREGKLLRLRLSRPKANIVDAEMIAALSAALGDAHEDSALRAVLIDHEGPHFSFGASVAEHMPD 77 
                                               8******************************************************************** PP

                                 TIGR03189  70 qcaamlkslhklviemldspvpilvavrgqclggglevaaagnllfaapdaklgqpeiklgvfapaasc 138
                                               qcaaml+slhklvi+m+d+p+pilvavrgqclgggleva+ag+++f++pdaklgqpei+lgvfapaasc
  lcl|NCBI__GCF_000009985.1:WP_011384541.1  78 QCAAMLASLHKLVIAMVDFPLPILVAVRGQCLGGGLEVALAGHMMFVSPDAKLGQPEIVLGVFAPAASC 146
                                               ********************************************************************* PP

                                 TIGR03189 139 llpervgkvaaedllysgrsidgaegariglvdavaedpeaaalayfdehlaklsasslrfavraarlg 207
                                               llper+++vaaedllysgrsidgae+ar+g+++av++dpe+aala+fd+++ak+sa+slrfav+aarlg
  lcl|NCBI__GCF_000009985.1:WP_011384541.1 147 LLPERMPRVAAEDLLYSGRSIDGAEAARLGIANAVVDDPENAALAWFDNGPAKHSAASLRFAVKAARLG 215
                                               ********************************************************************* PP

                                 TIGR03189 208 vvervkakiaevealyleelmathdaveglnaflekrpaawedr 251
                                               ++ervkakiaevealyl++lmathdaveglnaflekrpa+wedr
  lcl|NCBI__GCF_000009985.1:WP_011384541.1 216 MNERVKAKIAEVEALYLNGLMATHDAVEGLNAFLEKRPALWEDR 259
                                               *******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (259 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: 7.25
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources