Alignments for a candidate for aacS in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Marinobacter adhaerens HP15

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4237 HP15_4177 acetyl-CoA synthetase

Query= BRENDA::D6EQU8
         (658 letters)



>FitnessBrowser__Marino:GFF4237
          Length = 662

 Score =  561 bits (1445), Expect = e-164
 Identities = 283/653 (43%), Positives = 407/653 (62%), Gaps = 15/653 (2%)

Query: 2   STENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTE 61
           +T +P  LW P    +  +R+ +F+AW  E  G      Y AL++WS+DEL+TFW+ V +
Sbjct: 5   TTPSPDILWSPSEDTLKNSRMGQFKAWL-EQQGLGPFTDYHALYQWSIDELETFWQKVWD 63

Query: 62  WFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHEPA 120
           +  +   TP  +VLG R MPGA+WFPG  LN+A + LR A G   D+ A++   ET    
Sbjct: 64  YCGLVCDTPAEKVLGKRDMPGAEWFPGMKLNFAANLLRLADGEHADQEAVVAYCETRPVL 123

Query: 121 PVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDF 180
             T+A+L+    +L A LR  G++ GDRV+G + N  +A+V +LA  ++G +W+S +PDF
Sbjct: 124 RRTYAQLKADAGALEAFLRDKGIQQGDRVAGVVTNGYEALVGMLAATSMGAIWSSASPDF 183

Query: 181 GARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP 240
           G  ++LDRF Q+EP  L  V+GY YGGK   R+   AEL   LPTL++V+ +  L  E P
Sbjct: 184 GIGAILDRFGQIEPAALIVVNGYGYGGKVFARQQDFAELIAGLPTLKSVVSVQQLPDEPP 243

Query: 241 -DGTL--DWETLTAADA--EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295
             G L   WE + A      P +  +P DHP+++LYSSGTTG PK IV    G+LV H K
Sbjct: 244 IAGNLVTTWEDMLAYGKGNAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAK 303

Query: 296 QLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERT 355
           +L LH D+GP DRF ++T+ GWMMWN+  S L+TG  ++  DGSPG+P+ +  W      
Sbjct: 304 ELMLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEE 363

Query: 356 GATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADL 415
             T FGTSA ++  CRK  + PA+ LD S ++ V +TGSPL P+ + W++ +   G  D 
Sbjct: 364 KVTHFGTSARFIAGCRKGELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSD---GAPDA 420

Query: 416 WIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNP 475
            + S++GGTD+C CF G+ P LPV  GE+Q   LG D  ++   G P+++  GELV   P
Sbjct: 421 LLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSEGRGELVCRQP 480

Query: 476 MPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRM 535
           +PSMP+ FW DP   RY D+YF+T+PGVW HGD+I  T  G  +I+GRSD+TLN  GVR+
Sbjct: 481 LPSMPVSFWQDPGDERYKDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDATLNPGGVRI 540

Query: 536 GSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNL 595
           G+A+IY  VE + E+++SLV+G  Q DG   + L V  A G  + + LL ++K  IR   
Sbjct: 541 GTAEIYRQVETVAEVKDSLVVG-RQIDGDVEVVLLVVPAAGQEITNDLLKQLKSRIREGA 599

Query: 596 SPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTP----LDKAVNPGSIDNL 644
           SPRHVP  +++V  IP+T +GK++E+ V RL+ G+      D   NP ++D +
Sbjct: 600 SPRHVPKRIVQVNDIPYTRSGKKVELAVARLINGSKKSDNRDALSNPEALDEI 652


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: 1418
Number of extensions: 69
Number of successful extensions: 5
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: 662
Length adjustment: 38
Effective length of query: 620
Effective length of database: 624
Effective search space:   386880
Effective search space used:   386880
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 GFF4237 HP15_4177 (acetyl-CoA synthetase)
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.27000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-242  792.3   0.0     2e-242  791.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF4237  HP15_4177 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4237  HP15_4177 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  791.9   0.0    2e-242    2e-242       3     642 ..       9     650 ..       7     657 .. 0.97

  Alignments for each domain:
  == domain 1  score: 791.9 bits;  conditional E-value: 2e-242
                           TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGa.algdydalyrwsvdeldafwkavwefsdvvfssaekevvddskm 76 
                                         +++lw p ++  k++r+ +f+a+  ++ G+  ++dy aly+ws+del++fw++vw+++++v++++ ++v++++ m
  lcl|FitnessBrowser__Marino:GFF4237   9 PDILWSPSEDTLKNSRMGQFKAWLEQQ-GLgPFTDYHALYQWSIDELETFWQKVWDYCGLVCDTPAEKVLGKRDM 82 
                                         679********************9665.6659******************************************* PP

                           TIGR01217  77 laarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylp 147
                                         ++a++fpg +ln+a nllr ++     ++a++   e++ + + t+++l++    l+a lr  G+++Gdrvag++ 
  lcl|FitnessBrowser__Marino:GFF4237  83 PGAEWFPGMKLNFAANLLRLADGehadQEAVVAYCETRPVLRRTYAQLKADAGALEAFLRDKGIQQGDRVAGVVT 157
                                         *******************8876566556677778899999********************************** PP

                           TIGR01217 148 nipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlrav 222
                                         n  ea++ +la++s+Gaiwss+spdfG  ++ldrf+qiep  l++v+gy y+Gk   r++  +e+  +lp+l++v
  lcl|FitnessBrowser__Marino:GFF4237 158 NGYEALVGMLAATSMGAIWSSASPDFGIGAILDRFGQIEPAALIVVNGYGYGGKVFARQQDFAELIAGLPTLKSV 232
                                         *************************************************************************** PP

                           TIGR01217 223 vlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkeh 297
                                         v +  + d+  +a   +   t+ed+la  + + + f  lp dhp+yil+ssGttG pk+ivh + G+lv+h ke+
  lcl|FitnessBrowser__Marino:GFF4237 233 VSVQQLPDEPPIAG--NLVTTWEDMLAYGKGNAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAKEL 305
                                         ******98888887..55679*******9********************************************** PP

                           TIGR01217 298 vlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrk 372
                                          lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++  dGsp+ p+ n l+d ++ e++t +Gtsa+++  +rk
  lcl|FitnessBrowser__Marino:GFF4237 306 MLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEEKVTHFGTSARFIAGCRK 380
                                         *************************************************************************** PP

                           TIGR01217 373 kglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglG 447
                                         ++lkpa+t+d s lr+v stGspl pe +++vy+  ++d ll+si+GGtdi+ cfvg++p+lpv +Geiq++ lG
  lcl|FitnessBrowser__Marino:GFF4237 381 GELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSDGAPDALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLG 455
                                         *************************************************************************** PP

                           TIGR01217 448 laveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsd 522
                                         ++  a+ ++G+pv + +Gelv+ +plpsmpv fw d+   +y++ayf+++pgvwahGd+ie+t +Gg +i+Grsd
  lcl|FitnessBrowser__Marino:GFF4237 456 VDAVAYGDDGQPVSEGRGELVCRQPLPSMPVSFWQDPGDERYKDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSD 530
                                         *************************************************************************** PP

                           TIGR01217 523 atlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhv 597
                                         atlnp+Gvr+G+aeiy +ve + ev++slv+g+ q dg++ vvl+v  a+G++++++l+k++k++ir g+sprhv
  lcl|FitnessBrowser__Marino:GFF4237 531 ATLNPGGVRIGTAEIYRQVETVAEVKDSLVVGR-QIDGDVEVVLLVVPAAGQEITNDLLKQLKSRIREGASPRHV 604
                                         ********************************7.5799************************************* PP

                           TIGR01217 598 pskiievagiprtlsGkkvevavkdvvaG.kpvenkgalsnpeald 642
                                         p++i++v++ip+t sGkkve+av ++++G k  +n++alsnpeald
  lcl|FitnessBrowser__Marino:GFF4237 605 PKRIVQVNDIPYTRSGKKVELAVARLINGsKKSDNRDALSNPEALD 650
                                         ****************************944567***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (662 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: 00:00:00.03
# Mc/sec: 12.12
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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

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 catabolism of small carbon sources