GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Escherichia coli BW25113

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 14473 b0335 predicted propionyl-CoA synthetase with ATPase domain (NCBI)

Query= BRENDA::P77495
         (628 letters)



>lcl|FitnessBrowser__Keio:14473 b0335 predicted propionyl-CoA
           synthetase with ATPase domain (NCBI)
          Length = 628

 Score = 1279 bits (3309), Expect = 0.0
 Identities = 628/628 (100%), Positives = 628/628 (100%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR
Sbjct: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
           WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE
Sbjct: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD
Sbjct: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180

Query: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240
           AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT
Sbjct: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240

Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300
           SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG
Sbjct: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300

Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360
           MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY
Sbjct: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360

Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420
           LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN
Sbjct: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420

Query: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG 480
           VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG
Sbjct: 421 VQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDWG 480

Query: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540
           IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF
Sbjct: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540

Query: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600
           VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA
Sbjct: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600

Query: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628
           ICEGRDPGDLTTIDDPASLDQIRQAMEE
Sbjct: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628


Lambda     K      H
   0.320    0.136    0.422 

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: 1440
Number of extensions: 33
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: 628
Length of database: 628
Length adjustment: 38
Effective length of query: 590
Effective length of database: 590
Effective search space:   348100
Effective search space used:   348100
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: 54 (25.4 bits)

Align candidate 14473 b0335 (predicted propionyl-CoA synthetase with ATPase domain (NCBI))
to HMM TIGR02316 (prpE: propionate--CoA ligase (EC 6.2.1.17))

# 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/TIGR02316.hmm
# target sequence database:        /tmp/gapView.20946.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02316  [M=628]
Accession:   TIGR02316
Description: propion_prpE: propionate--CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1308.6   0.3          0 1308.4   0.3    1.0  1  lcl|FitnessBrowser__Keio:14473  b0335 predicted propionyl-CoA sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14473  b0335 predicted propionyl-CoA synthetase with ATPase domain (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1308.4   0.3         0         0       1     628 []       1     628 []       1     628 [] 1.00

  Alignments for each domain:
  == domain 1  score: 1308.4 bits;  conditional E-value: 0
                       TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalvavssetg 79 
                                     m+++e+yqrsi+epe+fwaeqarridwqtpf+++ld+sn+pfarwf++grtnlc+na+dr+lek++e+lal+avsset+
  lcl|FitnessBrowser__Keio:14473   1 MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRWLEKQPEALALIAVSSETE 79 
                                     79***************************************************************************** PP

                       TIGR02316  80 eertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashslaariddatpkl 158
                                     eert+t+rqlh+evna+as+lr+lgv+rgdrvl+y+pmiaea+++llacarigaihsvvfggfashs+aaridda+p+l
  lcl|FitnessBrowser__Keio:14473  80 EERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEAHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVL 158
                                     ******************************************************************************* PP

                       TIGR02316 159 ivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrrvpgrdvdyaalrrqhedadvevewlesnepsyi 237
                                     ivsadagarggk+i+ykklld+ai++aqh+p+hvllvdrglak++rv+grdvd+a+lr+qh++a+v+v+wlesne+s+i
  lcl|FitnessBrowser__Keio:14473 159 IVSADAGARGGKIIPYKKLLDDAISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCI 237
                                     ******************************************************************************* PP

                       TIGR02316 238 lytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdgg 316
                                     lytsgttgkpkgvqrdvggyavala+smd+ifg+kag+v+f+asd+gwvvghsyivyapllag+at++yeglpt+pd+g
  lcl|FitnessBrowser__Keio:14473 238 LYTSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGMATIVYEGLPTWPDCG 316
                                     ******************************************************************************* PP

                       TIGR02316 317 vwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpv 395
                                     vww+iveky+vs+mfsaptairvlkk+++a++rkhdlsslevl+lagepldepta+w+s++l++pvidnywqte+gwp+
  lcl|FitnessBrowser__Keio:14473 317 VWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPI 395
                                     ******************************************************************************* PP

                       TIGR02316 396 laiarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafkrlly 474
                                     +aiargldd+p++lgspg+p+ygy++++l+e+tge++g+nekg+lvv++plppgc++t+wgdd+rf+kty+s+f+r++y
  lcl|FitnessBrowser__Keio:14473 396 MAIARGLDDRPTRLGSPGVPMYGYNVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVY 474
                                     ******************************************************************************* PP

                       TIGR02316 475 ssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedad 553
                                     +++dwgird+dgy+filgrtddvinvaghrlgtreiees+ssh++vaevavvgvkd+lkgqvavaf+i+ke+ds+ed+d
  lcl|FitnessBrowser__Keio:14473 475 ATFDWGIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAFVIPKESDSLEDRD 553
                                     ******************************************************************************* PP

                       TIGR02316 554 dahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaaleqvrealee 628
                                     +ah++ek++malv+sq+g+++rpa+v++v++lpktrsgk+lrr+iqa++egrdpgdlttiddpa+l+q+r+a+ee
  lcl|FitnessBrowser__Keio:14473 554 VAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQAICEGRDPGDLTTIDDPASLDQIRQAMEE 628
                                     *************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (628 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.67
//
[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:

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:

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:

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, or view the source code.

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