Alignments for a candidate for prpE in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Dyella japonica UNC79MFTsu3.2

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate N515DRAFT_0016 N515DRAFT_0016 propionyl-CoA synthetase

Query= BRENDA::P77495
         (628 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0016
          Length = 630

 Score =  771 bits (1992), Expect = 0.0
 Identities = 370/628 (58%), Positives = 475/628 (75%), Gaps = 5/628 (0%)

Query: 1   MSFSEFYQRSINEPEQFWAEQARRIDWQTPFTQTLDHSNPPFARWFCEGRTNLCHNAIDR 60
           M +  FY+ SI  PE FWAEQA+ IDWQTP  Q LD+S PPF RWF  G TNLC+NAIDR
Sbjct: 1   MDYETFYRHSIEAPEAFWAEQAQLIDWQTPPRQVLDYSRPPFRRWFVGGTTNLCYNAIDR 60

Query: 61  WLEKQPEALALIAVSSETEEERTFTFRQLHDEVNAVASMLRSLGVQRGDRVLVYMPMIAE 120
            LE + + LAL+A+S+ET   R  ++RQLH EVN  A++L +L VQRGDRV++Y+P IAE
Sbjct: 61  HLEARGDQLALVAISTETGLTRELSYRQLHREVNVFAAVLAALDVQRGDRVVIYLPNIAE 120

Query: 121 AHITLLACARIGAIHSVVFGGFASHSVAARIDDAKPVLIVSADAGARGGKIIPYKKLLDD 180
           A   +LACAR+GAIHSVVFGGFA+H++A RIDDA+P L+++ADAG RGGK+IPYK L+D 
Sbjct: 121 AVFAMLACARLGAIHSVVFGGFAAHNLALRIDDAQPKLLIAADAGMRGGKVIPYKPLVDA 180

Query: 181 AISQAQHQPRHVLLVDRGL-AKMARVSGRDVDFASLRHQHIGARVPVAWLESNETSCILY 239
           A+ Q+   P HVL+VDRGL  +M RV+GRD+D+A LR  H  A VPVAWLESNE S +LY
Sbjct: 181 ALEQSAAPPPHVLIVDRGLDPQMTRVAGRDLDYAQLRKAHEQAEVPVAWLESNEPSYLLY 240

Query: 240 TSGTTGKPKGVQRDVGGYAVALATSMDTIFGGKAGSVFFCASDIGWVVGHSYIVYAPLLA 299
           TSGTTGKPKG+QRDVGGYAVA+A S+  IF    G V F  SD+GW VGHSY VY PL+A
Sbjct: 241 TSGTTGKPKGIQRDVGGYAVAMAMSVRYIFDIAPGQVMFSTSDVGWAVGHSYNVYGPLIA 300

Query: 300 GMATIVYEGLPTWPDCGVWWTIVEKYQVSRMFSAPTAIRVLKKFPTAEIRKHDLSSLEVL 359
           G  +++YEGLPT PD G+WW + E+Y V  MFS+PT IRVLKK   A +RK+DLSSL+ L
Sbjct: 301 GATSLLYEGLPTRPDPGIWWYLCERYSVRTMFSSPTGIRVLKKQDPAWLRKYDLSSLQWL 360

Query: 360 YLAGEPLDEPTASWVSNTLDVPVIDNYWQTESGWPIMAIARGLDDRPTRLGSPGVPMYGY 419
           +LAGEPLDEPTA W+++ L VPVIDNYWQTE+GWP + +  GL+ +  + GSPG+P  GY
Sbjct: 361 FLAGEPLDEPTAHWITDGLGVPVIDNYWQTETGWPAITLMPGLELKRVKFGSPGLPAPGY 420

Query: 420 NVQLLNEVTGEPCGVNEKGMLVVEGPLPPGCIQTIWGDDGRFVKTYWSLFSRPVYATFDW 479
            +++++E TGE      KG+LV E PLPPGC+ T+WGDD R++ +Y+  F   +Y++ DW
Sbjct: 421 RMKVIDEATGEEAAPGHKGVLVFEPPLPPGCLSTVWGDDERYLSSYFGHFKELLYSSLDW 480

Query: 480 GIRDADGYHFILGRTDDVINVAGHRLGTREIEESISSHPGVAEVAVVGVKDALKGQVAVA 539
            IRD  GY  ILGRTDDVINVAGHRLGTREIEES+++HP VAE AV+GV+D LKGQV V 
Sbjct: 481 AIRDEHGYTTILGRTDDVINVAGHRLGTREIEESVATHPAVAEAAVIGVRDELKGQVPVV 540

Query: 540 FVIPKESDSLEDRDVAHSQEKAIMALVDSQIGNFGRPAHVWFVSQLPKTRSGKMLRRTIQ 599
           F   K+    +   VA + ++ ++     Q+G   RP+ V+ V+ LPKTRSGK+LRR++Q
Sbjct: 541 FATLKQDAGTQAGQVAQAMQQRVV----DQLGGIARPSRVYVVNALPKTRSGKLLRRSLQ 596

Query: 600 AICEGRDPGDLTTIDDPASLDQIRQAME 627
           A+ E RDPGDL+T+DDP +L++IR+A+E
Sbjct: 597 ALAEQRDPGDLSTLDDPGALEEIRRALE 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: 1237
Number of extensions: 45
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: 630
Length adjustment: 38
Effective length of query: 590
Effective length of database: 592
Effective search space:   349280
Effective search space used:   349280
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 N515DRAFT_0016 N515DRAFT_0016 (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.27643.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 1154.0   0.0          0 1153.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016  N515DRAFT_0016 propionyl-CoA syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0016  N515DRAFT_0016 propionyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1153.8   0.0         0         0       1     628 []       1     625 [.       1     625 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1153.8 bits;  conditional E-value: 0
                                    TIGR02316   1 mayeelyqrsieepeafwaeqarridwqtpfarvlddsnlpfarwfvggrtnlcynavdrhlekrg 66 
                                                  m ye +y+ sie peafwaeqa+ idwqtp+ +vld+s++pf+rwfvgg tnlcyna+drhle rg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016   1 MDYETFYRHSIEAPEAFWAEQAQLIDWQTPPRQVLDYSRPPFRRWFVGGTTNLCYNAIDRHLEARG 66 
                                                  68**************************************************************** PP

                                    TIGR02316  67 eqlalvavssetgeertltyrqlhrevnalasalralgvrrgdrvliylpmiaeaalallacarig 132
                                                  +qlalva+s+etg +r+l+yrqlhrevn++a++l al v+rgdrv+iylp+iaea++a+lacar+g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016  67 DQLALVAISTETGLTRELSYRQLHREVNVFAAVLAALDVQRGDRVVIYLPNIAEAVFAMLACARLG 132
                                                  ****************************************************************** PP

                                    TIGR02316 133 aihsvvfggfashslaariddatpklivsadagarggkvieykklldaaiaeaqhkpahvllvdrg 198
                                                  aihsvvfggfa+h+la+ridda+pkl+++adag+rggkvi+yk+l+daa++++  +p+hvl+vdrg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 133 AIHSVVFGGFAAHNLALRIDDAQPKLLIAADAGMRGGKVIPYKPLVDAALEQSAAPPPHVLIVDRG 198
                                                  ****************************************************************** PP

                                    TIGR02316 199 lak.lrrvpgrdvdyaalrrqhedadvevewlesnepsyilytsgttgkpkgvqrdvggyavalaa 263
                                                  l++ ++rv+grd+dya lr+ he+a+v+v+wlesnepsy+lytsgttgkpkg+qrdvggyava+a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 199 LDPqMTRVAGRDLDYAQLRKAHEQAEVPVAWLESNEPSYLLYTSGTTGKPKGIQRDVGGYAVAMAM 264
                                                  **99************************************************************** PP

                                    TIGR02316 264 smdaifgakagdvlfsasdvgwvvghsyivyapllaglatvlyeglptrpdggvwwsivekyrvsv 329
                                                  s+  if++  g+v+fs+sdvgw+vghsy+vy+pl+ag++++lyeglptrpd+g+ww ++e+y v++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 265 SVRYIFDIAPGQVMFSTSDVGWAVGHSYNVYGPLIAGATSLLYEGLPTRPDPGIWWYLCERYSVRT 330
                                                  ****************************************************************** PP

                                    TIGR02316 330 mfsaptairvlkkqdaallrkhdlsslevlflagepldeptarwisdalgkpvidnywqtetgwpv 395
                                                  mfs+pt+irvlkkqd+a+lrk+dlssl++lflagepldepta+wi+d+lg+pvidnywqtetgwp 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 331 MFSSPTGIRVLKKQDPAWLRKYDLSSLQWLFLAGEPLDEPTAHWITDGLGVPVIDNYWQTETGWPA 396
                                                  ****************************************************************** PP

                                    TIGR02316 396 laiarglddkpvklgspglpvygyrldvldeatgedvgpnekgllvvaaplppgclstvwgddarf 461
                                                  +++++gl+ k vk+gspglp +gyr++v+deatge+++p+ kg+lv ++plppgclstvwgdd r+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 397 ITLMPGLELKRVKFGSPGLPAPGYRMKVIDEATGEEAAPGHKGVLVFEPPLPPGCLSTVWGDDERY 462
                                                  ****************************************************************** PP

                                    TIGR02316 462 lktyfsafkrllyssldwgirdedgytfilgrtddvinvaghrlgtreieesvsshaavaevavvg 527
                                                  l +yf++fk+llyssldw+irde gyt+ilgrtddvinvaghrlgtreieesv++h+avae+av+g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 463 LSSYFGHFKELLYSSLDWAIRDEHGYTTILGRTDDVINVAGHRLGTREIEESVATHPAVAEAAVIG 528
                                                  ****************************************************************** PP

                                    TIGR02316 528 vkdelkgqvavafailkeadsvedaddahalekelmalvesqlgavarparvyvvaalpktrsgkl 593
                                                  v+delkgqv+v+fa+lk+ +  +   +a  +++++++ v+ qlg +arp+rvyvv+alpktrsgkl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 529 VRDELKGQVPVVFATLKQDA--GT--QAGQVAQAMQQRVVDQLGGIARPSRVYVVNALPKTRSGKL 590
                                                  *****************433..33..34456678999***************************** PP

                                    TIGR02316 594 lrraiqavaegrdpgdlttiddpaaleqvrealee 628
                                                  lrr++qa+ae rdpgdl+t+ddp+ale++r+ale+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0016 591 LRRSLQALAEQRDPGDLSTLDDPGALEEIRRALER 625
                                                  *********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (628 nodes)
Target sequences:                          1  (630 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 9.30
//
[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