Alignments for a candidate for prpE in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Dokdonella koreensis DS-123

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_067644159.1 I596_RS03300 propionate--CoA ligase

Query= BRENDA::P77495
         (628 letters)



>NCBI__GCF_001632775.1:WP_067644159.1
          Length = 631

 Score =  766 bits (1979), Expect = 0.0
 Identities = 367/628 (58%), Positives = 471/628 (75%), Gaps = 5/628 (0%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           M + + Y++SI +PE FWAEQAR IDW  P  + L++++PPF RWF  G TNLCHNA+DR
Sbjct: 1   MRYEDVYRQSIEDPEGFWAEQARAIDWHVPPQRILEYTDPPFRRWFAGGLTNLCHNAVDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
            L  + + LAL+AVSSET   R  ++RQLH EVN  A+ L+SLGV RGDRV+VYMP +AE
Sbjct: 61  HLAARGDQLALVAVSSETGTTRKISYRQLHREVNTFAAALKSLGVGRGDRVVVYMPNMAE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           A   +LACARIGA+HSVVFGGFA+H++A RIDDAKP L+++ADAG RGG++IPYK L+D 
Sbjct: 121 AVFAMLACARIGAVHSVVFGGFAAHNLALRIDDAKPKLLIAADAGMRGGRVIPYKPLVDQ 180

Query: 181 AISQAQHQPRHVLLVDRGL-AKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILY 239
           A++ A   P HVL+V RGL    A V GRDVD+A LR ++  A VPV WLESNE S +LY
Sbjct: 181 ALAAAVSPPPHVLIVSRGLDPDPAWVQGRDVDYAPLRARYEDAEVPVEWLESNEPSYLLY 240

Query: 240 TSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLA 299
           TSGTTGKPKGVQRDVGGYAVA+A SM  ++    G V F  SD+GW VGHSY VY PL+ 
Sbjct: 241 TSGTTGKPKGVQRDVGGYAVAMALSMRAVYDVGPGQVMFSTSDVGWAVGHSYNVYGPLIV 300

Query: 300 GMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVL 359
           G  +++YEGLPT PD G+WW +   Y V  MFS+PT IRVLKK   A ++KHDL++L+ L
Sbjct: 301 GATSLLYEGLPTNPDPGIWWKLCADYGVRTMFSSPTGIRVLKKQDGAWLKKHDLTALKWL 360

Query: 360 YLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGY 419
           +LAGEPLDEPTA W+S+ L  P+IDNYWQTE+GWP++ +  GLD +P + GSPG+P  GY
Sbjct: 361 FLAGEPLDEPTAQWISDGLGKPIIDNYWQTETGWPVLTLLPGLDLKPVKFGSPGLPNLGY 420

Query: 420 NVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDW 479
            +++++EVTG      +KG+LV+E PLPPGC+ T+W DD RF+ +Y+S F   +Y++ DW
Sbjct: 421 KLRVIDEVTGADAAAGQKGVLVIEPPLPPGCMTTVWNDDQRFLSSYFSHFKELLYSSLDW 480

Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
            +RD DGY FILGRTDDVINVAGHRLGTREIEES+++HP VAE AVVGV DALKGQV V 
Sbjct: 481 AVRDEDGYTFILGRTDDVINVAGHRLGTREIEESVATHPSVAEAAVVGVHDALKGQVPVV 540

Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
           F   +++ +    D   S    ++  V  Q+G   RPA V+ V+ LPKTRSGK+LRR++Q
Sbjct: 541 FATLRQATA----DTPESAASGMLQCVVDQLGGVARPARVYVVNALPKTRSGKLLRRSLQ 596

Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAME 627
           A+ E RDPGDL+T+DDP +LD+ R+A+E
Sbjct: 597 ALAEDRDPGDLSTLDDPGALDECRRALE 624


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: 1233
Number of extensions: 46
Number of successful extensions: 4
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: 631
Length adjustment: 38
Effective length of query: 590
Effective length of database: 593
Effective search space:   349870
Effective search space used:   349870
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 WP_067644159.1 I596_RS03300 (propionate--CoA ligase)
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.2655545.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 1151.8   0.1          0 1151.7   0.1    1.0  1  NCBI__GCF_001632775.1:WP_067644159.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001632775.1:WP_067644159.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1151.7   0.1         0         0       1     628 []       1     625 [.       1     625 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1151.7 bits;  conditional E-value: 0
                             TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalva 73 
                                           m+ye++y++sie+pe fwaeqar+idw+ p++r+l+++++pf+rwf+gg tnlc+navdrhl+ rg+qlalva
  NCBI__GCF_001632775.1:WP_067644159.1   1 MRYEDVYRQSIEDPEGFWAEQARAIDWHVPPQRILEYTDPPFRRWFAGGLTNLCHNAVDRHLAARGDQLALVA 73 
                                           79*********************************************************************** PP

                             TIGR02316  74 vssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashs 146
                                           vssetg++r+++yrqlhrevn++a+al++lgv+rgdrv++y+p++aea++a+lacariga+hsvvfggfa+h+
  NCBI__GCF_001632775.1:WP_067644159.1  74 VSSETGTTRKISYRQLHREVNTFAAALKSLGVGRGDRVVVYMPNMAEAVFAMLACARIGAVHSVVFGGFAAHN 146
                                           ************************************************************************* PP

                             TIGR02316 147 laariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvpgrdvdyaalrrq 218
                                           la+ridda+pkl+++adag+rgg+vi+yk+l+d+a+a a+++p+hvl+v+rgl++  + v grdvdya lr +
  NCBI__GCF_001632775.1:WP_067644159.1 147 LALRIDDAKPKLLIAADAGMRGGRVIPYKPLVDQALAAAVSPPPHVLIVSRGLDPdPAWVQGRDVDYAPLRAR 219
                                           *******************************************************8899************** PP

                             TIGR02316 219 hedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsy 291
                                           +eda+v+vewlesnepsy+lytsgttgkpkgvqrdvggyava+a+sm a++++  g+v+fs+sdvgw+vghsy
  NCBI__GCF_001632775.1:WP_067644159.1 220 YEDAEVPVEWLESNEPSYLLYTSGTTGKPKGVQRDVGGYAVAMALSMRAVYDVGPGQVMFSTSDVGWAVGHSY 292
                                           ************************************************************************* PP

                             TIGR02316 292 ivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflage 364
                                           +vy+pl+ g++++lyeglpt+pd+g+ww+++  y+v++mfs+pt+irvlkkqd a+l+khdl++l++lflage
  NCBI__GCF_001632775.1:WP_067644159.1 293 NVYGPLIVGATSLLYEGLPTNPDPGIWWKLCADYGVRTMFSSPTGIRVLKKQDGAWLKKHDLTALKWLFLAGE 365
                                           ************************************************************************* PP

                             TIGR02316 365 pldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedvgpnek 437
                                           pldepta+wisd+lgkp+idnywqtetgwpvl++ +gld kpvk+gspglp  gy+l+v+de+tg d+++++k
  NCBI__GCF_001632775.1:WP_067644159.1 366 PLDEPTAQWISDGLGKPIIDNYWQTETGWPVLTLLPGLDLKPVKFGSPGLPNLGYKLRVIDEVTGADAAAGQK 438
                                           ************************************************************************* PP

                             TIGR02316 438 gllvvaaplppgclstvwgddarflktyfsafkrllyssldwgirdedgytfilgrtddvinvaghrlgtrei 510
                                           g+lv+++plppgc++tvw+dd rfl +yfs+fk+llyssldw++rdedgytfilgrtddvinvaghrlgtrei
  NCBI__GCF_001632775.1:WP_067644159.1 439 GVLVIEPPLPPGCMTTVWNDDQRFLSSYFSHFKELLYSSLDWAVRDEDGYTFILGRTDDVINVAGHRLGTREI 511
                                           ************************************************************************* PP

                             TIGR02316 511 eesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvva 583
                                           eesv++h++vae+avvgv+d+lkgqv+v+fa+l+     + ad++ + +++++++v+ qlg varparvyvv+
  NCBI__GCF_001632775.1:WP_067644159.1 512 EESVATHPSVAEAAVVGVHDALKGQVPVVFATLR----QATADTPESAASGMLQCVVDQLGGVARPARVYVVN 580
                                           **********************************....45678899999************************ PP

                             TIGR02316 584 alpktrsgkllrraiqavaegrdpgdlttiddpaaleqvrealee 628
                                           alpktrsgkllrr++qa+ae rdpgdl+t+ddp+al++ r+ale+
  NCBI__GCF_001632775.1:WP_067644159.1 581 ALPKTRSGKLLRRSLQALAEDRDPGDLSTLDDPGALDECRRALER 625
                                           ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (631 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: 39.49
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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