Alignments for a candidate for paaJ2 in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Sedimenticola selenatireducens DSM 17993

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_029134160.1 A3GO_RS0115385 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_000428045.1:WP_029134160.1
          Length = 403

 Score =  605 bits (1559), Expect = e-178
 Identities = 303/401 (75%), Positives = 345/401 (86%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+A I DA+RTPIGR+ GAL+ VRADDLGAIPLKAL+ R+P +DWS V+DVI+GCANQA
Sbjct: 1   MNDAYIFDAIRTPIGRFGGALSGVRADDLGAIPLKALMQRNPGVDWSQVEDVIFGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLP +VPGTT+NRLCGSG+DAV  AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPAAVPGTTVNRLCGSGMDAVSMAARAIKTGEAQLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVM K++ AF R AEI DTTIGWRFVNKLMQQ FGIDSMPETAENVA QF++SRAD
Sbjct: 121 SRAPFVMPKADSAFSRRAEIHDTTIGWRFVNKLMQQQFGIDSMPETAENVAEQFHVSRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ +  AA A+GRLA+EIV V + QRKG   +V  DEHPR DT LE+LA L T
Sbjct: 181 QDAFALRSQQRTGAAQASGRLAQEIVPVTLLQRKGEDIVVSSDEHPRPDTRLEKLASLPT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+GGSVTAGNASGVNDGACALLL S EA +R GL  +ARVV     GVEPRIMG GP 
Sbjct: 241 PFRKGGSVTAGNASGVNDGACALLLGSQEAGKRFGLSPKARVVAATAVGVEPRIMGFGPA 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PA+RK+L++TGL +  MDVIELNEAFAAQGLAV+R+LGLADD   VNPNGGAIALGHPLG
Sbjct: 301 PASRKLLQMTGLTIEQMDVIELNEAFAAQGLAVMRDLGLADDAAHVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTA+++L++  GRYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTAMYQLQQTGGRYALCTMCIGVGQGIALIIERV 401


Lambda     K      H
   0.319    0.134    0.384 

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: 578
Number of extensions: 14
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: 401
Length of database: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
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: 50 (23.9 bits)

Align candidate WP_029134160.1 A3GO_RS0115385 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.14461.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.1e-222  722.5   8.1     8e-222  722.3   8.1    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029134160.1  A3GO_RS0115385 3-oxoadipyl-CoA t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029134160.1  A3GO_RS0115385 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.3   8.1    8e-222    8e-222       2     400 .]       3     401 ..       2     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 722.3 bits;  conditional E-value: 8e-222
                                 TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 
                                               ++yi dairtpiGr+gG+ls vraddl+a+plkal++rnp +d+++++dvi+GcanqaGednrnvarm+
  lcl|NCBI__GCF_000428045.1:WP_029134160.1   3 DAYIFDAIRTPIGRFGGALSGVRADDLGAIPLKALMQRNPGVDWSQVEDVIFGCANQAGEDNRNVARMS 71 
                                               79******************************************************************* PP

                                 TIGR02430  71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139
                                               allaGlp++vpgttvnrlcgsg+da+++aaraik+Gea+l+iaGGvesmsrapfv+ kadsafsr+a++
  lcl|NCBI__GCF_000428045.1:WP_029134160.1  72 ALLAGLPAAVPGTTVNRLCGSGMDAVSMAARAIKTGEAQLMIAGGVESMSRAPFVMPKADSAFSRRAEI 140
                                               ********************************************************************* PP

                                 TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208
                                               +dttiGwrfvn  +++++G+dsmpetaenvae+f vsr+dqdafalrsqqrt aaqa+G +a+eivpv+
  lcl|NCBI__GCF_000428045.1:WP_029134160.1 141 HDTTIGWRFVNKLMQQQFGIDSMPETAENVAEQFHVSRADQDAFALRSQQRTGAAQASGRLAQEIVPVT 209
                                               ********************************************************************* PP

                                 TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277
                                               + q+kGe+ vv++deh+r++t le+la l +++r++g+vtaGnasGvndGa+alll s+ea kr+gl p
  lcl|NCBI__GCF_000428045.1:WP_029134160.1 210 LLQRKGEDIVVSSDEHPRPDTRLEKLASLPTPFRKGGSVTAGNASGVNDGACALLLGSQEAGKRFGLSP 278
                                               ********************************************************************* PP

                                 TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346
                                               +ar++aa+++Gvepr+mG+gp+pa +kll+ +gl++e++dvielneafaaq+lav+r+lgladd+a+vn
  lcl|NCBI__GCF_000428045.1:WP_029134160.1 279 KARVVAATAVGVEPRIMGFGPAPASRKLLQMTGLTIEQMDVIELNEAFAAQGLAVMRDLGLADDAAHVN 347
                                               ********************************************************************* PP

                                 TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               pnGGaialGhplG+sGarlv+ta++ql+++ggryal+t+ciGvGqGial+ierv
  lcl|NCBI__GCF_000428045.1:WP_029134160.1 348 PNGGAIALGHPLGMSGARLVTTAMYQLQQTGGRYALCTMCIGVGQGIALIIERV 401
                                               *****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (403 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: 8.33
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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