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.21899.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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.89
//
[ok]

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

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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