Alignments for a candidate for aacS in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Dechlorosoma suillum PS

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Dsui_2297 Dsui_2297 acetoacetyl-CoA synthase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__PS:Dsui_2297
          Length = 656

 Score =  797 bits (2058), Expect = 0.0
 Identities = 401/650 (61%), Positives = 471/650 (72%), Gaps = 7/650 (1%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P  E V  + +  F+    +       DYDA   WSV +  AFW+ +W+ C V+G+ 
Sbjct: 8   LWRPGPERVAAANLTRFMGAASQAAAAPLNDYDALWQWSVDQPAAFWSLLWDFCGVVGDK 67

Query: 67  GEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALVS 126
           G   L DGD+M  AR+FP+ RLN+AENLLR +G  DAL+F GEDKV   L+ DELRA VS
Sbjct: 68  GGTVLEDGDKMPGARWFPQGRLNYAENLLRFSGPEDALVFWGEDKVKRHLSRDELRAQVS 127

Query: 127 RLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQI 186
           R QQ L   G+  GDRVA  +PN+PET+  MLA AS+GAIWSS SPDFG QGVLDRFGQI
Sbjct: 128 RFQQFLEDAGVQPGDRVAGYLPNLPETLIAMLAAASLGAIWSSASPDFGVQGVLDRFGQI 187

Query: 187 APKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTLA 244
            PK+ +  DGYWYNGK  D  +K    A  L      V+VPY   +  +   +   VT  
Sbjct: 188 GPKVLVCVDGYWYNGKAVDCLTKNAEAAAQLPTLEKVVVVPYLAATPDIG-AIPKAVTWD 246

Query: 245 DFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRD 304
             +A F A    F RLPF HPL+I++SSGTTGVPKCIVH  GG +LQHLKEH+    ++ 
Sbjct: 247 QALAPFSATAPAFARLPFSHPLFIMYSSGTTGVPKCIVHCHGGAVLQHLKEHQLQGDVKP 306

Query: 305 GERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAK 364
           G+R+FYFTTCGWMMWNWL SGLA GATL LYDGSPF   G VLFDYA AE    FGTSAK
Sbjct: 307 GDRVFYFTTCGWMMWNWLVSGLASGATLLLYDGSPFADQGKVLFDYADAEAMTHFGTSAK 366

Query: 365 YIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIVS 424
           +IDA  K G  P  TH L +LR + STGSPLSPEGF +VY  IKP++QLASISGGTDI+S
Sbjct: 367 FIDAAAKMGLKPRETHKLQALRSLFSTGSPLSPEGFDYVYRDIKPELQLASISGGTDIIS 426

Query: 425 CFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWNDPD 484
           CFVLG P  PV+RGEIQ  GLG+AVDV++D+G+PVR +KGELVCT+ FP MPV FWNDPD
Sbjct: 427 CFVLGAPTLPVYRGEIQCRGLGMAVDVFDDDGQPVRRQKGELVCTKPFPVMPVGFWNDPD 486

Query: 485 GAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMD 544
           GAKY AAYF+RF NVWCHGDFAE T H G+VI+GRSDATLNPGGVRIGTAEIY QVEQ++
Sbjct: 487 GAKYHAAYFERFPNVWCHGDFAELTEHNGMVIYGRSDATLNPGGVRIGTAEIYRQVEQLE 546

Query: 545 EVAEALCIGQDWE----DDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           EV E+L IGQDW     DDVRVVLFV+L  G+ L +AL+  IK +IR   +PRHVPAK++
Sbjct: 547 EVVESLVIGQDWPPGKYDDVRVVLFVKLRDGLTLDDALSVRIKEQIRRNTTPRHVPAKVV 606

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
            V DIPRTKSGKIVELAVR+VVH RPVKN EALANPEAL+ F    EL S
Sbjct: 607 QVRDIPRTKSGKIVELAVRNVVHQRPVKNVEALANPEALEEFRERPELAS 656


Lambda     K      H
   0.322    0.139    0.441 

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: 1475
Number of extensions: 59
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: 650
Length of database: 656
Length adjustment: 38
Effective length of query: 612
Effective length of database: 618
Effective search space:   378216
Effective search space used:   378216
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate Dsui_2297 Dsui_2297 (acetoacetyl-CoA synthase)
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.11265.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-291  953.6   0.0   2.6e-291  953.4   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2297  Dsui_2297 acetoacetyl-CoA syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2297  Dsui_2297 acetoacetyl-CoA synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  953.4   0.0  2.6e-291  2.6e-291       5     650 ..       7     654 ..       3     656 .] 0.98

  Alignments for each domain:
  == domain 1  score: 953.4 bits;  conditional E-value: 2.6e-291
                         TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskmlaarf 81 
                                        lw+p  erv+ a+l+rf  a++++  a l dydal++wsvd+  afw+ +w+f++vv++++   + d++km++ar+
  lcl|FitnessBrowser__PS:Dsui_2297   7 LLWRPGPERVAAANLTRFMGAASQAAAAPLNDYDALWQWSVDQPAAFWSLLWDFCGVVGDKGGTVLEDGDKMPGARW 83 
                                       79*************************************************************************** PP

                         TIGR01217  82 fpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaalla 158
                                       fp+ rlnyaenllr +g edal++ +e+k++ +++ +elr+qv+++++ l   Gv++Gdrvagylpn+pe++ a+la
  lcl|FitnessBrowser__PS:Dsui_2297  84 FPQGRLNYAENLLRFSGPEDALVFWGEDKVKRHLSRDELRAQVSRFQQFLEDAGVQPGDRVAGYLPNLPETLIAMLA 160
                                       ***************************************************************************** PP

                         TIGR01217 159 tasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipyvgdrekla 235
                                       +as+Gaiwss+spdfG++gvldrf+qi pk+l++vdgy+ynGk  d   k +e a +lp+l++vv++py+  +   +
  lcl|FitnessBrowser__PS:Dsui_2297 161 AASLGAIWSSASPDFGVQGVLDRFGQIGPKVLVCVDGYWYNGKAVDCLTKNAEAAAQLPTLEKVVVVPYLAAT--PD 235
                                       ***********************************************************************55..55 PP

                         TIGR01217 236 p.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrlly 311
                                       +  ++ a+t+++ la + a+ + f +lpf+hpl+i++ssGttGvpk+ivh  GG ++qhlkeh+l +d+++gdr++y
  lcl|FitnessBrowser__PS:Dsui_2297 236 IgAIPKAVTWDQALAPFSATAPAFARLPFSHPLFIMYSSGTTGVPKCIVHCHGGAVLQHLKEHQLQGDVKPGDRVFY 312
                                       556************************************************************************** PP

                         TIGR01217 312 yttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrl 388
                                       +tt+Gwmmwn+lvsgla Gatl lydGsp+  +++vlfd+a++e +t +Gtsak+++a  k glkp +th+l+alr 
  lcl|FitnessBrowser__PS:Dsui_2297 313 FTTCGWMMWNWLVSGLASGATLLLYDGSPFADQGKVLFDYADAEAMTHFGTSAKFIDAAAKMGLKPRETHKLQALRS 389
                                       ***************************************************************************** PP

                         TIGR01217 389 vastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekG 465
                                       + stGspl+pegf+yvy+ ik++++lasisGGtdi+scfv++ p+lpvy+Geiq++glG+av+++d++G+pv+ +kG
  lcl|FitnessBrowser__PS:Dsui_2297 390 LFSTGSPLSPEGFDYVYRDIKPELQLASISGGTDIISCFVLGAPTLPVYRGEIQCRGLGMAVDVFDDDGQPVRRQKG 466
                                       ***************************************************************************** PP

                         TIGR01217 466 elvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynave 542
                                       elv+tkp+p mpv fwnd+dG+ky++ayf+++p+vw+hGd++elt + g+vi+Grsdatlnp+Gvr+G+aeiy +ve
  lcl|FitnessBrowser__PS:Dsui_2297 467 ELVCTKPFPVMPVGFWNDPDGAKYHAAYFERFPNVWCHGDFAELTEHNGMVIYGRSDATLNPGGVRIGTAEIYRQVE 543
                                       ***************************************************************************** PP

                         TIGR01217 543 rldeveeslvigqeqedg...eervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkv 616
                                       +l+ev eslvigq+++ g   ++rvvlfvkl  G tld+al  +ik++ir + +prhvp+k+++v++iprt+sGk+v
  lcl|FitnessBrowser__PS:Dsui_2297 544 QLEEVVESLVIGQDWPPGkydDVRVVLFVKLRDGLTLDDALSVRIKEQIRRNTTPRHVPAKVVQVRDIPRTKSGKIV 620
                                       ***************98744468****************************************************** PP

                         TIGR01217 617 evavkdvvaGkpvenkgalsnpealdlyeeleel 650
                                       e+av++vv+ +pv+n +al+npeal+ ++e +el
  lcl|FitnessBrowser__PS:Dsui_2297 621 ELAVRNVVHQRPVKNVEALANPEALEEFRERPEL 654
                                       *****************************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (656 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: 9.56
//
[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