Alignments for a candidate for paaJ2 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Marinobacter adhaerens HP15

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate GFF2751 HP15_2695 acetyl-CoA acetyltransferase

Query= reanno::Marino:GFF2751
         (415 letters)



>FitnessBrowser__Marino:GFF2751
          Length = 415

 Score =  811 bits (2094), Expect = 0.0
 Identities = 415/415 (100%), Positives = 415/415 (100%)

Query: 1   MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY 60
           MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY
Sbjct: 1   MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY 60

Query: 61  GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA 120
           GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA
Sbjct: 61  GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA 120

Query: 121 GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF 180
           GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF
Sbjct: 121 GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF 180

Query: 181 GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL 240
           GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL
Sbjct: 181 GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL 240

Query: 241 ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM 300
           ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM
Sbjct: 241 ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM 300

Query: 301 GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL 360
           GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL
Sbjct: 301 GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL 360

Query: 361 GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA 415
           GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA
Sbjct: 361 GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA 415


Lambda     K      H
   0.318    0.133    0.382 

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: 726
Number of extensions: 15
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: 415
Length of database: 415
Length adjustment: 31
Effective length of query: 384
Effective length of database: 384
Effective search space:   147456
Effective search space used:   147456
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: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF2751 HP15_2695 (acetyl-CoA acetyltransferase)
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.19665.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.8e-223  727.7   6.0   2.1e-223  727.5   6.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2751  HP15_2695 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2751  HP15_2695 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.5   6.0  2.1e-223  2.1e-223       1     400 []       8     411 ..       8     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 727.5 bits;  conditional E-value: 2.1e-223
                           TIGR02430   1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaG 75 
                                         k++yivdairtpiGrygG+ls+vraddl+a+p+kal +r+p+ld+++iddv++GcanqaGednr+varm++llaG
  lcl|FitnessBrowser__Marino:GFF2751   8 KDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNRDVARMSLLLAG 82 
                                         689************************************************************************ PP

                           TIGR02430  76 lpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvn 150
                                         lpv+vpg+t+nrlcgsg+da+g aarai++Ge++l+iaGGvesmsrapfv+Gkadsafsr+a+++dttiGwrfvn
  lcl|FitnessBrowser__Marino:GFF2751  83 LPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVN 157
                                         *************************************************************************** PP

                           TIGR02430 151 pklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehl 225
                                         p lk++yG+dsmpetaenva +fg+sredqdafalrsqqrtaaaq++G +a+ei+pv+i+++k ++ vvd+deh+
  lcl|FitnessBrowser__Marino:GFF2751 158 PVLKKQYGIDSMPETAENVAADFGISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHP 232
                                         *************************************************************************** PP

                           TIGR02430 226 raettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvp 300
                                         r et+le+la l +++re+gtvtaGnasGvndGa+allla+++a+k+++l+prar++a+a+aGvepr+mG+gp+p
  lcl|FitnessBrowser__Marino:GFF2751 233 R-ETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306
                                         *.************************************************************************* PP

                           TIGR02430 301 avkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqlek 375
                                         a++k+la agl+l+d+dvielneafaaqalav+r+lgl+dd+++vnpnGGaialGhplG+sGarlv+tal++le+
  lcl|FitnessBrowser__Marino:GFF2751 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGARLVTTALNELER 381
                                         *************************************************************************98 PP

                           TIGR02430 376 s.....ggryalatlciGvGqGialvierv 400
                                         +     + ryal+t+ciGvGqGial+ier+
  lcl|FitnessBrowser__Marino:GFF2751 382 RhaagqKARYALCTMCIGVGQGIALIIERM 411
                                         633222469*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (415 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: 9.76
//
[ok]

This GapMind analysis is from Sep 17 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