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 GFF3858 HP15_3799 acetyl-CoA synthetase

Query= BRENDA::D6EQU8
         (658 letters)



>FitnessBrowser__Marino:GFF3858
          Length = 662

 Score =  579 bits (1492), Expect = e-169
 Identities = 296/662 (44%), Positives = 414/662 (62%), Gaps = 15/662 (2%)

Query: 1   MSTENPQPL-WQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAV 59
           MS E   P+ W P    +A +R+ +F+AW  E  G      Y ALH+WS+DEL+TFW+ V
Sbjct: 1   MSNEEQSPVVWSPSEDTLANSRMGQFKAWL-EQQGFGPFADYHALHQWSIDELETFWQKV 59

Query: 60  TEWFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHE 118
            ++  +   TP  +VLG   MPGA+WFPG  LN+A + LR A G   D  A++   ET  
Sbjct: 60  WDYCGLVCDTPAEKVLGKHEMPGAEWFPGMKLNFAANLLRLADGEHRDREAVVAYCETRP 119

Query: 119 PAPVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAP 178
               T+AEL+    +L A LR+ G++ GDRV+G + N  +A+V +LA  ++G +W+S +P
Sbjct: 120 VLRRTYAELKADAGALEAFLRSKGIKQGDRVAGVVTNGYEALVGMLAATSLGAIWSSASP 179

Query: 179 DFGARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTE 238
           DFG  ++LDRF Q+EP  L  V+GY YGGK   R+   AEL   LPTL+AV+ +  L  E
Sbjct: 180 DFGIGAILDRFGQIEPSALIVVNGYGYGGKVFARQQDFAELIAGLPTLKAVVSVQQLPDE 239

Query: 239 AP---DGTLDWETLTAAD--AEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEH 293
           AP   D    WE   AA     P +  +P DHP+++LYSSGTTG PK IV    G+LV H
Sbjct: 240 APISGDLVTTWENALAAGEGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNH 299

Query: 294 LKQLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAE 353
            K+L LH D+GP DRF ++T+ GWMMWN+  S L+TG  ++  DGSPG+P+ +  W    
Sbjct: 300 AKELMLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVA 359

Query: 354 RTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGA 413
               T FGTSA ++  CRK  + PA+ LD S ++ V +TGSPL P+ + W++ +   G  
Sbjct: 360 EEKVTHFGTSARFIAGCRKGELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSD---GAP 416

Query: 414 DLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVT 473
           D  + S++GGTD+C CF G+ P LPV  GE+Q   LG D  ++   G P+++  GELV  
Sbjct: 417 DALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSEGRGELVCR 476

Query: 474 NPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGV 533
            P+PSMP+ FW DPDG RY D+YF+T+PGVW HGD+I  T  G  +I+GRSD+TLN  GV
Sbjct: 477 QPLPSMPVSFWQDPDGERYRDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDATLNPGGV 536

Query: 534 RMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRV 593
           R+G+A+IY  VE + E+++SLV+G  Q DG   + L V  A G  + D LL ++K  IR 
Sbjct: 537 RIGTAEIYRQVETVAEVKDSLVVG-RQIDGDVEVVLLVVPADGQEITDDLLKQLKSRIRE 595

Query: 594 NLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL-HFYEE 652
             SPRHVP  ++EV  IP+T +GK++E+ V RL+ G+   KA N  ++ N + L H  E 
Sbjct: 596 GASPRHVPKHIVEVNDIPYTRSGKKVELAVARLINGS--KKADNRDALGNPEALDHIRER 653

Query: 653 LA 654
           L+
Sbjct: 654 LS 655


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: 1456
Number of extensions: 82
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 GFF3858 HP15_3799 (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.24946.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.5e-246  804.8   0.0   3.2e-246  804.4   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3858  HP15_3799 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3858  HP15_3799 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.4   0.0  3.2e-246  3.2e-246       3     646 ..       7     652 ..       4     655 .. 0.97

  Alignments for each domain:
  == domain 1  score: 804.4 bits;  conditional E-value: 3.2e-246
                           TIGR01217   3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskml 77 
                                           v+w p ++  +++r+ +f+a+  ++    ++dy al++ws+del++fw++vw+++++v++++ ++v+++++m+
  lcl|FitnessBrowser__Marino:GFF3858   7 SPVVWSPSEDTLANSRMGQFKAWLEQQGFGPFADYHALHQWSIDELETFWQKVWDYCGLVCDTPAEKVLGKHEMP 81 
                                         4589*******************97776569******************************************** PP

                           TIGR01217  78 aarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148
                                         +a++fpg +ln+a nllr ++      +a++   e++ + + t++el++    l+a lr+ G+k+Gdrvag++ n
  lcl|FitnessBrowser__Marino:GFF3858  82 GAEWFPGMKLNFAANLLRLADGehrdREAVVAYCETRPVLRRTYAELKADAGALEAFLRSKGIKQGDRVAGVVTN 156
                                         ******************8876566545666667889999*********************************** PP

                           TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravv 223
                                           ea++ +la++s+Gaiwss+spdfG  ++ldrf+qiep  l++v+gy y+Gk   r++  +e+  +lp+l+avv
  lcl|FitnessBrowser__Marino:GFF3858 157 GYEALVGMLAATSLGAIWSSASPDFGIGAILDRFGQIEPSALIVVNGYGYGGKVFARQQDFAELIAGLPTLKAVV 231
                                         *************************************************************************** PP

                           TIGR01217 224 lipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehv 298
                                          +  + d++ ++   +   t+e+ laa + + + f  lp dhp+yil+ssGttG pk+ivh + G+lv+h ke+ 
  lcl|FitnessBrowser__Marino:GFF3858 232 SVQQLPDEAPISG--DLVTTWENALAAGEGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAKELM 304
                                         *****98777777..77889*******9*********************************************** PP

                           TIGR01217 299 lhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkk 373
                                         lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++  dGsp+ p+ n l+d ++ e++t +Gtsa+++  +rk+
  lcl|FitnessBrowser__Marino:GFF3858 305 LHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEEKVTHFGTSARFIAGCRKG 379
                                         *************************************************************************** PP

                           TIGR01217 374 glkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGl 448
                                         +lkpa+t+d s lr+v stGspl pe +++vy+  ++d ll+si+GGtdi+ cfvg++p+lpv +Geiq++ lG+
  lcl|FitnessBrowser__Marino:GFF3858 380 ELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSDGAPDALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGV 454
                                         *************************************************************************** PP

                           TIGR01217 449 aveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsda 523
                                         +  a+ ++G+pv + +Gelv+ +plpsmpv fw d+dG +yr+ayf+++pgvwahGd+ie+t +Gg +i+Grsda
  lcl|FitnessBrowser__Marino:GFF3858 455 DAVAYGDDGQPVSEGRGELVCRQPLPSMPVSFWQDPDGERYRDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDA 529
                                         *************************************************************************** PP

                           TIGR01217 524 tlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvp 598
                                         tlnp+Gvr+G+aeiy +ve + ev++slv+g+ q dg++ vvl+v  a G++++++l+k++k++ir g+sprhvp
  lcl|FitnessBrowser__Marino:GFF3858 530 TLNPGGVRIGTAEIYRQVETVAEVKDSLVVGR-QIDGDVEVVLLVVPADGQEITDDLLKQLKSRIREGASPRHVP 603
                                         *******************************7.5799************************************** PP

                           TIGR01217 599 skiievagiprtlsGkkvevavkdvvaG.kpvenkgalsnpealdlyee 646
                                         ++i+ev++ip+t sGkkve+av ++++G k  +n++al npeald  +e
  lcl|FitnessBrowser__Marino:GFF3858 604 KHIVEVNDIPYTRSGKKVELAVARLINGsKKADNRDALGNPEALDHIRE 652
                                         ***************************945678***********98765 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: 00:00:00.04
# Mc/sec: 10.29
//
[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:

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