GapMind for catabolism of small carbon sources

 

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.carbon/TIGR02316.hmm
# target sequence database:        /tmp/gapView.13789.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.87
//
[ok]

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

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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:

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:

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:

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:

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