GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Marinobacter algicola DG893

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_007155469.1 MDG893_RS19030 acetoacetate--CoA ligase

Query= BRENDA::D6EQU8
         (658 letters)



>NCBI__GCF_000170835.1:WP_007155469.1
          Length = 663

 Score =  560 bits (1444), Expect = e-164
 Identities = 286/652 (43%), Positives = 404/652 (61%), Gaps = 13/652 (1%)

Query: 2   STENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTE 61
           +TE    +W P    +    + +FQ W  E  G      Y ALHRWS++ L+TFW+ V +
Sbjct: 3   NTEQSPVVWSPSQDTLKHCLMGQFQGWL-EQQGFGPFADYHALHRWSIENLETFWQKVWD 61

Query: 62  WFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHEPA 120
           +  +   TP   VLG R MPGA+WFPG  LN+A + LR A G   +  A++   ET    
Sbjct: 62  YCGLVCDTPADAVLGKRDMPGAEWFPGMKLNFAANLLRLAEGDHAEREAVVAYCETRPVL 121

Query: 121 PVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDF 180
             T+AEL+    +L A LR  G+R GDRV+G + N  +A+V +LA  ++G VW+S +PDF
Sbjct: 122 RRTYAELKADTGALEAFLRKKGIRQGDRVAGVVTNGYEALVGMLAATSLGAVWSSASPDF 181

Query: 181 GARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTE-- 238
           G  ++LDRF Q+EP  L  V+GY YGGK  +R+D  A L   LP+LR V+ I  L  E  
Sbjct: 182 GVGAILDRFGQIEPAALIVVNGYGYGGKVFNRQDDFAGLIDGLPSLRCVVSIEQLPGEPA 241

Query: 239 -APDGTLDWETLTAADA--EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295
            A D    W+   A      P +  +P +HP+++LYSSGTTG PK IV    G+LV H K
Sbjct: 242 VAGDKVTHWDEALAEGQGQAPSFTPLPPEHPVYILYSSGTTGKPKCIVHGNAGLLVNHAK 301

Query: 296 QLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERT 355
           +L LH D+GP DRF ++T+ GWMMWN+  S LLTG  ++  DGSPG+P  +  W++    
Sbjct: 302 ELMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPDLNYLWQVVADE 361

Query: 356 GATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADL 415
             T +GTSA ++  CRKA + PA++LDL+A++ V +TGSPL P+ + W++ +   G  D+
Sbjct: 362 KVTHYGTSARFIAGCRKAELTPAKNLDLTALRVVFSTGSPLLPEDYDWIYSD---GAPDV 418

Query: 416 WIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNP 475
            + S++GGTD+C CF G+ P LPV  GE+Q   LG D  ++   G P++   GELV   P
Sbjct: 419 LLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSGGRGELVCRQP 478

Query: 476 MPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRM 535
           +PSMP+ FW+DP   RY D+YF+T+P VW HGD+I  T  G  VI+GRSD+TLN  GVR+
Sbjct: 479 LPSMPVAFWDDPGNERYKDAYFNTFPDVWAHGDFIEFTEHGGAVIYGRSDATLNPGGVRI 538

Query: 536 GSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNL 595
           G+A+IY  VE + E+++SLV+G  Q +G   + L V  A G  L D L   +K  IR   
Sbjct: 539 GTAEIYRQVETVAEVKDSLVVG-RQIEGDVEVVLLVVPAEGQALTDDLQKNLKTRIRQGA 597

Query: 596 SPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL 647
           SPRHVP  +I+VP IP+T +GK++E+ V RL+ G+  +KA N  ++ N + L
Sbjct: 598 SPRHVPKHIIQVPDIPYTRSGKKVELAVARLINGS--NKADNRDALGNPEAL 647


Lambda     K      H
   0.320    0.138    0.442 

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: 1463
Number of extensions: 80
Number of successful extensions: 6
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: 658
Length of database: 663
Length adjustment: 38
Effective length of query: 620
Effective length of database: 625
Effective search space:   387500
Effective search space used:   387500
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_007155469.1 MDG893_RS19030 (acetoacetate--CoA ligase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

# 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/TIGR01217.hmm
# target sequence database:        /tmp/gapView.3452309.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01217  [M=652]
Accession:   TIGR01217
Description: ac_ac_CoA_syn: acetoacetate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-242  792.4   0.0   1.8e-242  792.0   0.0    1.0  1  NCBI__GCF_000170835.1:WP_007155469.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170835.1:WP_007155469.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.0   0.0  1.8e-242  1.8e-242       3     646 ..       7     652 ..       5     657 .. 0.97

  Alignments for each domain:
  == domain 1  score: 792.0 bits;  conditional E-value: 1.8e-242
                             TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 
                                             v+w p ++  k++ + +f+ +  ++    ++dy al+rws+++l++fw++vw+++++v++++ ++v++++ 
  NCBI__GCF_000170835.1:WP_007155469.1   7 SPVVWSPSQDTLKHCLMGQFQGWLEQQGFGPFADYHALHRWSIENLETFWQKVWDYCGLVCDTPADAVLGKRD 79 
                                           5689*******************97776569****************************************** PP

                             TIGR01217  76 mlaarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvag 144
                                           m++a++fpg +ln+a nllr ++      +a++   e++ + + t++el++    l+a lr+ G+++Gdrvag
  NCBI__GCF_000170835.1:WP_007155469.1  80 MPGAEWFPGMKLNFAANLLRLAEGdhaeREAVVAYCETRPVLRRTYAELKADTGALEAFLRKKGIRQGDRVAG 152
                                           ********************99875554345666678899999****************************** PP

                             TIGR01217 145 ylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelp 217
                                           ++ n  ea++ +la++s+Ga+wss+spdfG+ ++ldrf+qiep  l++v+gy y+Gk  +r++  + +  +lp
  NCBI__GCF_000170835.1:WP_007155469.1 153 VVTNGYEALVGMLAATSLGAVWSSASPDFGVGAILDRFGQIEPAALIVVNGYGYGGKVFNRQDDFAGLIDGLP 225
                                           ************************************************************************* PP

                             TIGR01217 218 dlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtl 290
                                           +lr vv i  +  + ++a   +   ++++ la  q   + f  lp +hp+yil+ssGttG pk+ivh + G+l
  NCBI__GCF_000170835.1:WP_007155469.1 226 SLRCVVSIEQLPGEPAVAG--DKVTHWDEALAEGQGQAPSFTPLPPEHPVYILYSSGTTGKPKCIVHGNAGLL 296
                                           *********9997777777..9999************************************************ PP

                             TIGR01217 291 vqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGts 363
                                           v+h ke+ lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++  dGsp+ p+ n l+++++ e++t +Gts
  NCBI__GCF_000170835.1:WP_007155469.1 297 VNHAKELMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPDLNYLWQVVADEKVTHYGTS 369
                                           ************************************************************************* PP

                             TIGR01217 364 akyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpv 436
                                           a+++  +rk++l+pa+++dl+alr+v stGspl pe ++++y+  ++dvll+si+GGtdi+ cfvg++p+lpv
  NCBI__GCF_000170835.1:WP_007155469.1 370 ARFIAGCRKAELTPAKNLDLTALRVVFSTGSPLLPEDYDWIYSDGAPDVLLGSIAGGTDICGCFVGSTPLLPV 442
                                           ************************************************************************* PP

                             TIGR01217 437 ykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyiel 509
                                            +Geiq++ lG++  a+ ++G+pv g +Gelv+ +plpsmpv fw+d+   +y++ayf+++p+vwahGd+ie+
  NCBI__GCF_000170835.1:WP_007155469.1 443 RRGEIQCRFLGVDAVAYGDDGQPVSGGRGELVCRQPLPSMPVAFWDDPGNERYKDAYFNTFPDVWAHGDFIEF 515
                                           ************************************************************************* PP

                             TIGR01217 510 tprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvk 582
                                           t +Gg vi+Grsdatlnp+Gvr+G+aeiy +ve + ev++slv+g++ e g++ vvl+v  a+G+ l+++l k
  NCBI__GCF_000170835.1:WP_007155469.1 516 TEHGGAVIYGRSDATLNPGGVRIGTAEIYRQVETVAEVKDSLVVGRQIE-GDVEVVLLVVPAEGQALTDDLQK 587
                                           *********************************************8765.7********************** PP

                             TIGR01217 583 eikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkp.venkgalsnpealdlyee 646
                                           ++k +ir g+sprhvp++ii+v++ip+t sGkkve+av ++++G    +n++al npeald  +e
  NCBI__GCF_000170835.1:WP_007155469.1 588 NLKTRIRQGASPRHVPKHIIQVPDIPYTRSGKKVELAVARLINGSNkADNRDALGNPEALDRIRE 652
                                           ********************************************76267***********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (663 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.29
//
[ok]

This GapMind analysis is from Sep 24 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