Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate H281DRAFT_04471 H281DRAFT_04471 propionyl-CoA synthetase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__Burk376:H281DRAFT_04471
          Length = 635

 Score =  800 bits (2066), Expect = 0.0
 Identities = 387/627 (61%), Positives = 484/627 (77%), Gaps = 1/627 (0%)

Query: 3   FSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDRWL 62
           + +F++RSI  PE FW ++ARRI W+TPF   LD SNPPFARWF  GRTNLCHNA+DR L
Sbjct: 4   YRDFHRRSIENPEAFWRDEARRIHWETPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRHL 63

Query: 63  EKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAEAH 122
             + +  AL+ VS+ET  ER +T+ +L+ E+N +A+++RSLGV+RGD VL+Y+PMI EA 
Sbjct: 64  VDRAQQNALVYVSTETGIERRYTYAELYAEINRMAAVMRSLGVKRGDVVLLYLPMIPEAL 123

Query: 123 ITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDDAI 182
             +LACAR+GAIHSVVFGGFA+ ++AARIDDAKPVLIV+ADAGARGGK+I Y  L+D+AI
Sbjct: 124 FAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDYTPLVDEAI 183

Query: 183 SQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYTSG 242
           ++A H+   VLL+DR LA     +   VD+  LR Q   A V   WLES+E S +LYTSG
Sbjct: 184 ARATHKTARVLLIDRQLAPERLNATYLVDYEPLREQFFDAHVSCEWLESSEPSYVLYTSG 243

Query: 243 TTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAGMA 302
           TTGKPKGVQRDVGGYAVALA SM+ IF GKAG   F ASD+GWVVGHSYIVYAPL+AG+ 
Sbjct: 244 TTGKPKGVQRDVGGYAVALAASMEYIFEGKAGDTMFTASDVGWVVGHSYIVYAPLIAGLT 303

Query: 303 TIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLYLA 362
           T++YEG P  PD G+WW +VE+++++ MF+APTA+RVLKK   A +   DLSSL  L+LA
Sbjct: 304 TVMYEGTPIRPDGGIWWRLVEQHKINLMFTAPTALRVLKKQDPALLESADLSSLRTLFLA 363

Query: 363 GEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYNVQ 422
           GEPLDEPTASW++  L  PVIDNYWQTE+GWP++AI RG++  PT+LGSPGVP  G+N+ 
Sbjct: 364 GEPLDEPTASWITGALGKPVIDNYWQTETGWPMLAIPRGVEALPTKLGSPGVPSAGFNLT 423

Query: 423 LLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLF-SRPVYATFDWGI 481
           L NE+TGEPC   EKG+L +  PLPPGC+ T+WGDD RF+ TYWS F  + VY+TFDWGI
Sbjct: 424 LRNELTGEPCPPGEKGVLTLNYPLPPGCMSTVWGDDKRFISTYWSSFPDQQVYSTFDWGI 483

Query: 482 RDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVAFV 541
           +D DGY  ILGRTDDVINVAGHRLGTREIEE++SSH  VAEVAVVGV D LKGQ A+AFV
Sbjct: 484 QDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGVADPLKGQAAMAFV 543

Query: 542 IPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQAI 601
           + +++ +  D D     E  + A VD Q+G   RP+ V  VS LPKTRSGK+LRR I A+
Sbjct: 544 VLRDAQAYADVDARTKLEAELTATVDRQLGAIARPSRVVIVSMLPKTRSGKLLRRAIAAL 603

Query: 602 CEGRDPGDLTTIDDPASLDQIRQAMEE 628
            EGR+PG+L TI+DPA+L Q+R+ + E
Sbjct: 604 AEGREPGELPTIEDPAALQQVREGLSE 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: 1165
Number of extensions: 39
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: 635
Length adjustment: 38
Effective length of query: 590
Effective length of database: 597
Effective search space:   352230
Effective search space used:   352230
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 H281DRAFT_04471 H281DRAFT_04471 (propionyl-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.aa/TIGR02316.hmm
# target sequence database:        /tmp/gapView.20859.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 1102.3   0.1          0 1102.0   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04471  H281DRAFT_04471 propionyl-CoA sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04471  H281DRAFT_04471 propionyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1102.0   0.1         0         0       2     627 ..       3     629 ..       2     630 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1102.0 bits;  conditional E-value: 0
                                    TIGR02316   2 ayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrge 67 
                                                  +y+++++rsie+peafw ++arri+w+tpf +vld sn+pfarwfvggrtnlc+navdrhl +r++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471   3 RYRDFHRRSIENPEAFWRDEARRIHWETPFDTVLDRSNPPFARWFVGGRTNLCHNAVDRHLVDRAQ 68 
                                                  7***************************************************************** PP

                                    TIGR02316  68 qlalvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacariga 133
                                                  q alv+vs+etg+er +ty +l+ e+n++a+++r+lgv+rgd vl+ylpmi+ea +a+lacar+ga
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471  69 QNALVYVSTETGIERRYTYAELYAEINRMAAVMRSLGVKRGDVVLLYLPMIPEALFAMLACARLGA 134
                                                  ****************************************************************** PP

                                    TIGR02316 134 ihsvvfggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrgl 199
                                                  ihsvvfggfa+ +laaridda+p+liv+adagarggkvi+y +l+d+aia+a hk a vll+dr+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 135 IHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDYTPLVDEAIARATHKTARVLLIDRQL 200
                                                  ****************************************************************** PP

                                    TIGR02316 200 aklrrvpgrdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasm 265
                                                  a+ r  +   vdy  lr+q  da+v +ewles+epsy+lytsgttgkpkgvqrdvggyavalaasm
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 201 APERLNATYLVDYEPLREQFFDAHVSCEWLESSEPSYVLYTSGTTGKPKGVQRDVGGYAVALAASM 266
                                                  ****************************************************************** PP

                                    TIGR02316 266 daifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsvmf 331
                                                  + if++kagd++f+asdvgwvvghsyivyapl+agl+tv+yeg+p+rpdgg+ww++ve+++++ mf
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 267 EYIFEGKAGDTMFTASDVGWVVGHSYIVYAPLIAGLTTVMYEGTPIRPDGGIWWRLVEQHKINLMF 332
                                                  ****************************************************************** PP

                                    TIGR02316 332 saptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpvla 397
                                                  +apta+rvlkkqd+all   dlssl++lflagepldepta+wi+ algkpvidnywqtetgwp+la
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 333 TAPTALRVLKKQDPALLESADLSSLRTLFLAGEPLDEPTASWITGALGKPVIDNYWQTETGWPMLA 398
                                                  ****************************************************************** PP

                                    TIGR02316 398 iarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarflk 463
                                                  i+rg++  p+klgspg+p  g++l + +e tge++ p+ekg+l+++ plppgc+stvwgdd rf+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 399 IPRGVEALPTKLGSPGVPSAGFNLTLRNELTGEPCPPGEKGVLTLNYPLPPGCMSTVWGDDKRFIS 464
                                                  ****************************************************************** PP

                                    TIGR02316 464 tyfsafk.rllyssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvgv 528
                                                  ty+s f+ + +ys++dwgi+dedgy++ilgrtddvinvaghrlgtreiee++sshaavaevavvgv
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 465 TYWSSFPdQQVYSTFDWGIQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGV 530
                                                  ******9899******************************************************** PP

                                    TIGR02316 529 kdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvvaalpktrsgkll 594
                                                  +d+lkgq a+af++l++a++ +d d++  le+el a+v++qlga+arp+rv +v+ lpktrsgkll
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 531 ADPLKGQAAMAFVVLRDAQAYADVDARTKLEAELTATVDRQLGAIARPSRVVIVSMLPKTRSGKLL 596
                                                  ****************************************************************** PP

                                    TIGR02316 595 rraiqavaegrdpgdlttiddpaaleqvreale 627
                                                  rrai a+aegr+pg+l ti+dpaal+qvre l 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04471 597 RRAIAALAEGREPGELPTIEDPAALQQVREGLS 629
                                                  *****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (635 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: 00:00:00.04
# Mc/sec: 8.12
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis