Alignments for a candidate for prpE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Burkholderia phytofirmans PsJN

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate BPHYT_RS13830 BPHYT_RS13830 acetyl-CoA synthetase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__BFirm:BPHYT_RS13830
          Length = 634

 Score =  802 bits (2071), Expect = 0.0
 Identities = 386/628 (61%), Positives = 490/628 (78%), Gaps = 1/628 (0%)

Query: 2   SFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRW 61
           S+ +F++RSI +PE FW ++ARRI W TPF   LD SNPPFARWF  GRTNLCHNA+DR 
Sbjct: 3   SYRDFHRRSIEDPEAFWRDEARRIHWHTPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRH 62

Query: 62  LEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEA 121
           L ++ +  AL+ VS+ET  ER +T+ +L+ EVN +A+++RSL V+RGD VL+Y+PMI EA
Sbjct: 63  LAERAQQNALVYVSTETGIERRYTYAELYGEVNRMAAVMRSLDVKRGDVVLLYLPMIPEA 122

Query: 122 HITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDA 181
              +LACAR+GAIHSVVFGGFA+ ++AARIDDAKPVLIV+ADAGARGGK+I Y  L+D+A
Sbjct: 123 LFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDYTPLMDEA 182

Query: 182 ISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYTS 241
           +++AQH+   VLL+DR LA     +   V +  LR Q   A VP  WLESNE S +LYTS
Sbjct: 183 LARAQHKTPRVLLIDRQLAPERLNASYLVAYEPLREQFFDAHVPCEWLESNEPSYVLYTS 242

Query: 242 GTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGM 301
           GTTGKPKGVQRDVGGYAVALA SM+ IF GKAG V F ASD+GWVVGHSYIVYAPL+AG+
Sbjct: 243 GTTGKPKGVQRDVGGYAVALAASMEHIFQGKAGDVMFTASDVGWVVGHSYIVYAPLIAGL 302

Query: 302 ATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYL 361
            T++YEG P  PD G+WW +V  ++++ MF+APTA+RVLKK   A +++ DL+SL  L+L
Sbjct: 303 TTVMYEGTPIRPDGGIWWRLVAHHRINLMFTAPTALRVLKKQDPALLKQADLTSLRALFL 362

Query: 362 AGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYNV 421
           AGEPLDEPTA+W++  LD PVIDNYWQTE+GWP++AI RG++  PTRLGSPGVP  G+N+
Sbjct: 363 AGEPLDEPTAAWIAGALDKPVIDNYWQTETGWPMLAIPRGVEALPTRLGSPGVPSAGFNL 422

Query: 422 QLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYW-SLFSRPVYATFDWG 480
            L NE+TGEPC   EKG+L ++ PLPPGC+ T+WGDD RFV TYW S+ ++ VY+TFDWG
Sbjct: 423 TLRNELTGEPCPPGEKGVLTLDYPLPPGCMSTVWGDDKRFVSTYWSSIPNQQVYSTFDWG 482

Query: 481 IRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAF 540
           ++D DGY  ILGRTDDVINVAGHRLGTREIEE++SSH  VAEVAVVGV D LKGQ A+AF
Sbjct: 483 VQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGVTDPLKGQAAMAF 542

Query: 541 VIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQA 600
           V+ +++ +  D       +  + A VD Q+G   RP+ V  V  LPKTRSGK+LRR I A
Sbjct: 543 VVLRDAQAYADTKKRSKLDAELTATVDRQLGAIARPSRVVVVPMLPKTRSGKLLRRAIAA 602

Query: 601 ICEGRDPGDLTTIDDPASLDQIRQAMEE 628
           + EGR+PGDL TI+DPA+L Q+R+A+++
Sbjct: 603 LAEGREPGDLPTIEDPAALQQVREALDD 630


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: 1182
Number of extensions: 38
Number of successful extensions: 2
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: 634
Length adjustment: 38
Effective length of query: 590
Effective length of database: 596
Effective search space:   351640
Effective search space used:   351640
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 BPHYT_RS13830 BPHYT_RS13830 (acetyl-CoA synthetase)
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.12846.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 1095.7   0.1          0 1095.5   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13830  BPHYT_RS13830 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13830  BPHYT_RS13830 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1095.5   0.1         0         0       2     627 ..       3     629 ..       2     630 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1095.5 bits;  conditional E-value: 0
                                TIGR02316   2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlal 71 
                                              +y+++++rsie+peafw ++arri+w+tpf +vld sn+pfarwfvggrtnlc+navdrhl++r++q al
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830   3 SYRDFHRRSIEDPEAFWRDEARRIHWHTPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRHLAERAQQNAL 72 
                                              7********************************************************************* PP

                                TIGR02316  72 vavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfgg 141
                                              v+vs+etg+er +ty +l+ evn++a+++r+l v+rgd vl+ylpmi+ea +a+lacar+gaihsvvfgg
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830  73 VYVSTETGIERRYTYAELYGEVNRMAAVMRSLDVKRGDVVLLYLPMIPEALFAMLACARLGAIHSVVFGG 142
                                              ********************************************************************** PP

                                TIGR02316 142 fashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrrvpgrdvd 211
                                              fa+ +laaridda+p+liv+adagarggkvi+y +l+d+a+a+aqhk + vll+dr+la+ r  ++  v 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 143 FAAPNLAARIDDAKPVLIVTADAGARGGKVIDYTPLMDEALARAQHKTPRVLLIDRQLAPERLNASYLVA 212
                                              ********************************************************************** PP

                                TIGR02316 212 yaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsas 281
                                              y  lr+q  da+v++ewlesnepsy+lytsgttgkpkgvqrdvggyavalaasm+ if++kagdv+f+as
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 213 YEPLREQFFDAHVPCEWLESNEPSYVLYTSGTTGKPKGVQRDVGGYAVALAASMEHIFQGKAGDVMFTAS 282
                                              ********************************************************************** PP

                                TIGR02316 282 dvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkh 351
                                              dvgwvvghsyivyapl+agl+tv+yeg+p+rpdgg+ww++v ++r++ mf+apta+rvlkkqd+all++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 283 DVGWVVGHSYIVYAPLIAGLTTVMYEGTPIRPDGGIWWRLVAHHRINLMFTAPTALRVLKKQDPALLKQA 352
                                              ********************************************************************** PP

                                TIGR02316 352 dlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrl 421
                                              dl+sl+ lflagepldepta wi+ al+kpvidnywqtetgwp+lai+rg++  p++lgspg+p  g++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 353 DLTSLRALFLAGEPLDEPTAAWIAGALDKPVIDNYWQTETGWPMLAIPRGVEALPTRLGSPGVPSAGFNL 422
                                              ********************************************************************** PP

                                TIGR02316 422 dvldeatgedvgpnekgllvvaaplppgclstvwgddarflktyfsafk.rllyssldwgirdedgytfi 490
                                               + +e tge++ p+ekg+l++  plppgc+stvwgdd rf+ ty+s ++ + +ys++dwg++dedgy++i
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 423 TLRNELTGEPCPPGEKGVLTLDYPLPPGCMSTVWGDDKRFVSTYWSSIPnQQVYSTFDWGVQDEDGYVTI 492
                                              ***********************************************99899****************** PP

                                TIGR02316 491 lgrtddvinvaghrlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddahalek 560
                                              lgrtddvinvaghrlgtreiee++sshaavaevavvgv+d+lkgq a+af++l++a++ +d++++  l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 493 LGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGVTDPLKGQAAMAFVVLRDAQAYADTKKRSKLDA 562
                                              ********************************************************************** PP

                                TIGR02316 561 elmalvesqlgavarparvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaaleqvreale 627
                                              el a+v++qlga+arp+rv vv  lpktrsgkllrrai a+aegr+pgdl ti+dpaal+qvreal+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13830 563 ELTATVDRQLGAIARPSRVVVVPMLPKTRSGKLLRRAIAALAEGREPGDLPTIEDPAALQQVREALD 629
                                              *****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (634 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.99
//
[ok]

This GapMind analysis is from Sep 17 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