Alignments for a candidate for prpE in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Stenotrophomonas chelatiphaga DSM 21508

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_057507018.1 ABB28_RS02085 propionate--CoA ligase

Query= BRENDA::P77495
         (628 letters)



>NCBI__GCF_001431535.1:WP_057507018.1
          Length = 626

 Score =  760 bits (1963), Expect = 0.0
 Identities = 366/627 (58%), Positives = 472/627 (75%), Gaps = 4/627 (0%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           M + E Y+RSI+EPE FW E+A RI W  P  Q LD+SNPPF RW+  G TNLC+NA+DR
Sbjct: 1   MDYEETYRRSIDEPEAFWGEEANRIYWHKPPRQVLDYSNPPFRRWYVGGETNLCYNAVDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
            L ++P+ LAL+AVS+ET   R  T+RQL+ EVN  A++L+ L V  GDRV++YMP +AE
Sbjct: 61  HLAERPDQLALVAVSTETGTTREITYRQLYREVNDFAAVLKRLDVGHGDRVVIYMPNMAE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           A   +LACARIGA+HSVVFGGFA+H++A RIDDA+P L+++ADAG RGGK+IPYK ++D 
Sbjct: 121 AVFAMLACARIGAVHSVVFGGFAAHNLALRIDDARPKLLIAADAGMRGGKLIPYKGMVDA 180

Query: 181 AISQAQHQPRHVLLVDRGLAKMA-RVSGRDVDFASLRHQHIGARVPVAWLESNETSCILY 239
           A ++AQ+ P HVL+V RGL     R +GRDVD+A+LR +     VPV WLES+E S +LY
Sbjct: 181 ACAEAQNPPPHVLIVSRGLDPAEPRQAGRDVDYATLRAEVGEVDVPVQWLESSEPSYLLY 240

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

Query: 300 GMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVL 359
           G  +++YEGLPT PD G+WW + E+Y V  +FS+PTAIRVLKK     IR+HDL +L+ +
Sbjct: 301 GCTSLLYEGLPTNPDPGIWWALCEQYNVRTLFSSPTAIRVLKKHDVDFIRRHDLKALKYI 360

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

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

Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
            IRD DGY FILGRTDDVINVAGHRLGTREIEE+IS HP VAE AV+GVKD LKGQV + 
Sbjct: 481 AIRDEDGYTFILGRTDDVINVAGHRLGTREIEEAISGHPRVAEAAVIGVKDELKGQVPLV 540

Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
           FV  K+  + ED     ++   +MA V + +G   RPAH+  V+ LPKTRSGK+LRR++Q
Sbjct: 541 FVTLKQGLNGEDPAPVVAE---MMAAVTASLGAVARPAHIHVVNALPKTRSGKLLRRSLQ 597

Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAM 626
           A+ E RDPGDL+T+DDPA+LD+IR+A+
Sbjct: 598 ALAEQRDPGDLSTLDDPAALDEIRRAL 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: 1216
Number of extensions: 43
Number of successful extensions: 3
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: 626
Length adjustment: 38
Effective length of query: 590
Effective length of database: 588
Effective search space:   346920
Effective search space used:   346920
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_057507018.1 ABB28_RS02085 (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.11860.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 1114.1   0.0          0 1113.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057507018.1  ABB28_RS02085 propionate--CoA li


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507018.1  ABB28_RS02085 propionate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1113.9   0.0         0         0       1     627 [.       1     625 [.       1     626 [] 0.98

  Alignments for each domain:
  == domain 1  score: 1113.9 bits;  conditional E-value: 0
                                 TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeql 69 
                                               m yee y+rsi+epeafw+e+a+ri w+ p+ +vld+sn+pf+rw+vgg+tnlcynavdrhl++r++ql
  lcl|NCBI__GCF_001431535.1:WP_057507018.1   1 MDYEETYRRSIDEPEAFWGEEANRIYWHKPPRQVLDYSNPPFRRWYVGGETNLCYNAVDRHLAERPDQL 69 
                                               68******************************************************************* PP

                                 TIGR02316  70 alvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvv 138
                                               alvavs+etg++r++tyrql+revn +a++l+ l v+ gdrv+iy+p++aea++a+lacariga+hsvv
  lcl|NCBI__GCF_001431535.1:WP_057507018.1  70 ALVAVSTETGTTREITYRQLYREVNDFAAVLKRLDVGHGDRVVIYMPNMAEAVFAMLACARIGAVHSVV 138
                                               ********************************************************************* PP

                                 TIGR02316 139 fggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglak.lrrvp 206
                                               fggfa+h+la+ridda+pkl+++adag+rggk+i+yk ++daa+aeaq++p+hvl+v+rgl++   r +
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 139 FGGFAAHNLALRIDDARPKLLIAADAGMRGGKLIPYKGMVDAACAEAQNPPPHVLIVSRGLDPaEPRQA 207
                                               ***************************************************************556889 PP

                                 TIGR02316 207 grdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagd 275
                                               grdvdya+lr +  + dv+v+wles+epsy+lytsgttgkpkgvqrdvggyava+a sm+++f+ + g+
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 208 GRDVDYATLRAEVGEVDVPVQWLESSEPSYLLYTSGTTGKPKGVQRDVGGYAVAMAQSMQTVFDCQPGQ 276
                                               ********************************************************************* PP

                                 TIGR02316 276 vlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqd 344
                                               v+fs+sdvgw+vghsy+vy+pl+ g +++lyeglpt+pd+g+ww+++e+y+v+++fs+ptairvlkk+d
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 277 VMFSTSDVGWAVGHSYNVYGPLIGGCTSLLYEGLPTNPDPGIWWALCEQYNVRTLFSSPTAIRVLKKHD 345
                                               ********************************************************************* PP

                                 TIGR02316 345 aallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspg 413
                                                  +r+hdl +l+++flagepldepta+w ++algkp+idnywqtetgwp l++ +gld kpv++gspg
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 346 VDFIRRHDLKALKYIFLAGEPLDEPTAHWANEALGKPIIDNYWQTETGWPALTLLPGLDMKPVRFGSPG 414
                                               ********************************************************************* PP

                                 TIGR02316 414 lpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafkrllyssldwgir 482
                                               +p  gyr++v+de tg +v+p++kg+lv+++plppgc+stvw+ddarfl++yfs+fk+llyssldw+ir
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 415 FPNLGYRMKVIDENTGVEVAPGQKGVLVMTPPLPPGCMSTVWNDDARFLQSYFSHFKELLYSSLDWAIR 483
                                               ********************************************************************* PP

                                 TIGR02316 483 dedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsved 551
                                               dedgytfilgrtddvinvaghrlgtreiee++s h+ vae+av+gvkdelkgqv+++f++lk+  + e 
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 484 DEDGYTFILGRTDDVINVAGHRLGTREIEEAISGHPRVAEAAVIGVKDELKGQVPLVFVTLKQGLNGE- 551
                                               **************************************************************665544. PP

                                 TIGR02316 552 addahalekelmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaale 620
                                                 d+  + +e+ma+v + lgavarpa+++vv+alpktrsgkllrr++qa+ae rdpgdl+t+ddpaal+
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 552 --DPAPVVAEMMAAVTASLGAVARPAHIHVVNALPKTRSGKLLRRSLQALAEQRDPGDLSTLDDPAALD 618
                                               ..55667789*********************************************************** PP

                                 TIGR02316 621 qvreale 627
                                               ++r+al 
  lcl|NCBI__GCF_001431535.1:WP_057507018.1 619 EIRRALG 625
                                               *****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (626 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.74
//
[ok]

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

Downloads

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

Related tools

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