Alignments for a candidate for prpE in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Azohydromonas australica DSM 1124

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_028998090.1 H537_RS0111790 propionate--CoA ligase

Query= BRENDA::P77495
         (628 letters)



>NCBI__GCF_000430725.1:WP_028998090.1
          Length = 637

 Score =  827 bits (2135), Expect = 0.0
 Identities = 396/630 (62%), Positives = 498/630 (79%), Gaps = 8/630 (1%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           M++++F+QRSI + E FWAEQA+ I+W  PF Q  D+S  PF RWF  G TNLCHNA+DR
Sbjct: 1   MTYADFHQRSIQQREDFWAEQAKLIEWNKPFDQVCDYSRAPFVRWFPGGETNLCHNAVDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
            L+ +P+  AL+ VS+E  +E+ ++FR+LH EV  +A++L+SLGV++GDRVL+YMPMI E
Sbjct: 61  HLKDRPDQNALVWVSTEVGKEQAYSFRELHAEVQRMAAVLQSLGVKQGDRVLLYMPMIPE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           A   +LA  R+GAIHSVVFGGFASHS+A+RI+D+ P ++VSAD G+RGGK+IPYK LLD+
Sbjct: 121 AVFAMLAAVRLGAIHSVVFGGFASHSLASRIEDSSPTVVVSADGGSRGGKVIPYKPLLDE 180

Query: 181 AISQAQHQPRHVLLVDRGLAKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILYT 240
           A+  + H+P  VLLVDRGLA M R  GRDVD+A+ R Q +  +VPV W+++   S  LYT
Sbjct: 181 ALRLSSHKPAKVLLVDRGLAPMERTEGRDVDYAAAREQVLDTQVPVTWVDATHPSYTLYT 240

Query: 241 SGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLAG 300
           SGTTGKPKGVQRD GGY VALA S+  IF G+ G  F C SDIGWVVGHSYIVY PL+ G
Sbjct: 241 SGTTGKPKGVQRDTGGYTVALAASIPHIFMGQPGETFLCTSDIGWVVGHSYIVYGPLIGG 300

Query: 301 MATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVLY 360
           M TI+YEGLPT PD GVWW++VEKY+ + MFSAPTA+RVLKK   A ++K+DLSSL+ L+
Sbjct: 301 MTTILYEGLPTTPDAGVWWSLVEKYKATVMFSAPTAVRVLKKHDPALLKKYDLSSLKALF 360

Query: 361 LAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGYN 420
           LAGEPLDEPTA W+S+ L  P+IDNYWQTE+GWPI++IA G++ +P++ GSPGVP YGY+
Sbjct: 361 LAGEPLDEPTARWISDGLGCPIIDNYWQTETGWPILSIANGVEKQPSKFGSPGVPTYGYD 420

Query: 421 VQLLNEVTGEP-CGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYW----SLFSRP--- 472
           V+L+++ TGE   G ++KG++VVEGPLPPGC+QT+WGDD RFVKTYW    +L  +P   
Sbjct: 421 VKLIDQQTGEELAGADQKGVVVVEGPLPPGCLQTVWGDDDRFVKTYWQKVPALDGKPERW 480

Query: 473 VYATFDWGIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDAL 532
           +Y+TFDWGIRD DGY+FILGRTDDVINVAGHRLGTREIEESI SH  VAEVAVVGV D L
Sbjct: 481 LYSTFDWGIRDKDGYYFILGRTDDVINVAGHRLGTREIEESICSHAAVAEVAVVGVADQL 540

Query: 533 KGQVAVAFVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGK 592
           KGQVA+AF + +++ +L D       E  IM  VD+Q+G   RPA V FVS LPKTRSGK
Sbjct: 541 KGQVAMAFAVLRDATALGDEARLAQLEGEIMKTVDAQLGAVARPARVRFVSVLPKTRSGK 600

Query: 593 MLRRTIQAICEGRDPGDLTTIDDPASLDQI 622
           +LRR IQA+CE RDPGDLTT++DPA+L QI
Sbjct: 601 LLRRAIQAVCEQRDPGDLTTMEDPAALRQI 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: 1188
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: 637
Length adjustment: 38
Effective length of query: 590
Effective length of database: 599
Effective search space:   353410
Effective search space used:   353410
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_028998090.1 H537_RS0111790 (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.aa/TIGR02316.hmm
# target sequence database:        /tmp/gapView.2122074.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 1079.6   0.4          0 1079.3   0.4    1.0  1  NCBI__GCF_000430725.1:WP_028998090.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_028998090.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1079.3   0.4         0         0       1     623 [.       1     631 [.       1     635 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1079.3 bits;  conditional E-value: 0
                             TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrgeqlalva 73 
                                           m+y +++qrsi++ e fwaeqa+ i+w+ pf +v d+s+ pf rwf gg+tnlc+navdrhl++r++q alv 
  NCBI__GCF_000430725.1:WP_028998090.1   1 MTYADFHQRSIQQREDFWAEQAKLIEWNKPFDQVCDYSRAPFVRWFPGGETNLCHNAVDRHLKDRPDQNALVW 73 
                                           78*********************************************************************** PP

                             TIGR02316  74 vssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarigaihsvvfggfashs 146
                                           vs+e g+e+ +++r+lh ev+++a++l++lgv++gdrvl+y+pmi+ea++a+la  r+gaihsvvfggfashs
  NCBI__GCF_000430725.1:WP_028998090.1  74 VSTEVGKEQAYSFRELHAEVQRMAAVLQSLGVKQGDRVLLYMPMIPEAVFAMLAAVRLGAIHSVVFGGFASHS 146
                                           ************************************************************************* PP

                             TIGR02316 147 laariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrglaklrrvpgrdvdyaalrrqh 219
                                           la ri+d+ p ++vsad g+rggkvi+yk+lld+a+  + hkpa+vllvdrgla+++r+ grdvdyaa r+q 
  NCBI__GCF_000430725.1:WP_028998090.1 147 LASRIEDSSPTVVVSADGGSRGGKVIPYKPLLDEALRLSSHKPAKVLLVDRGLAPMERTEGRDVDYAAAREQV 219
                                           ************************************************************************* PP

                             TIGR02316 220 edadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaasmdaifgakagdvlfsasdvgwvvghsyi 292
                                            d++v+v w++++ psy lytsgttgkpkgvqrd+ggy+valaas++ if ++ g++++++sd+gwvvghsyi
  NCBI__GCF_000430725.1:WP_028998090.1 220 LDTQVPVTWVDATHPSYTLYTSGTTGKPKGVQRDTGGYTVALAASIPHIFMGQPGETFLCTSDIGWVVGHSYI 292
                                           ************************************************************************* PP

                             TIGR02316 293 vyapllaglatvlyeglptrpdggvwwsivekyrvsvmfsaptairvlkkqdaallrkhdlsslevlflagep 365
                                           vy+pl+ g++t+lyeglpt+pd+gvwws+veky+ +vmfsapta+rvlkk+d+all+k+dlssl+ lflagep
  NCBI__GCF_000430725.1:WP_028998090.1 293 VYGPLIGGMTTILYEGLPTTPDAGVWWSLVEKYKATVMFSAPTAVRVLKKHDPALLKKYDLSSLKALFLAGEP 365
                                           ************************************************************************* PP

                             TIGR02316 366 ldeptarwisdalgkpvidnywqtetgwpvlaiarglddkpvklgspglpvygyrldvldeatgedv.gpnek 437
                                           ldeptarwisd+lg p+idnywqtetgwp+l+ia+g++++p+k+gspg+p ygy+++++d+ tge+  g+++k
  NCBI__GCF_000430725.1:WP_028998090.1 366 LDEPTARWISDGLGCPIIDNYWQTETGWPILSIANGVEKQPSKFGSPGVPTYGYDVKLIDQQTGEELaGADQK 438
                                           ****************************************************************99726789* PP

                             TIGR02316 438 gllvvaaplppgclstvwgddarflktyfsaf.......krllyssldwgirdedgytfilgrtddvinvagh 503
                                           g++vv++plppgcl+tvwgdd rf+kty+ +        +r lys++dwgird+dgy filgrtddvinvagh
  NCBI__GCF_000430725.1:WP_028998090.1 439 GVVVVEGPLPPGCLQTVWGDDDRFVKTYWQKVpaldgkpERWLYSTFDWGIRDKDGYYFILGRTDDVINVAGH 511
                                           *****************************9763333322478******************************* PP

                             TIGR02316 504 rlgtreieesvsshaavaevavvgvkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarp 576
                                           rlgtreiees++shaavaevavvgv+d+lkgqva+afa+l++a++++d++    le+e+m++v++qlgavarp
  NCBI__GCF_000430725.1:WP_028998090.1 512 RLGTREIEESICSHAAVAEVAVVGVADQLKGQVAMAFAVLRDATALGDEARLAQLEGEIMKTVDAQLGAVARP 584
                                           ************************************************************************* PP

                             TIGR02316 577 arvyvvaalpktrsgkllrraiqavaegrdpgdlttiddpaaleqvr 623
                                           arv +v+ lpktrsgkllrraiqav+e rdpgdltt++dpaal q+ 
  NCBI__GCF_000430725.1:WP_028998090.1 585 ARVRFVSVLPKTRSGKLLRRAIQAVCEQRDPGDLTTMEDPAALRQIS 631
                                           ********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (637 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 35.61
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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