Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Cupriavidus basilensis 4G11

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate RR42_RS10085 RR42_RS10085 acetoacetyl-CoA synthase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__Cup4G11:RR42_RS10085
          Length = 1020

 Score =  441 bits (1134), Expect = e-128
 Identities = 267/652 (40%), Positives = 346/652 (53%), Gaps = 25/652 (3%)

Query: 6   PLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAV--WEHCKVI 63
           P++    E    S M  F        G+ F DYD  HD+SV E   FW     W H    
Sbjct: 10  PIYGSTSERAAASQMTAFTTALQAYTGQVFGDYDTLHDFSVREYRTFWQCFVQWSHGLAW 69

Query: 64  GESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGD---ALIFRGEDKVSYRLTWDE 120
             S E   V GD    ARFFP+ +LN+A+NLL +  +     AL     D    RLT  E
Sbjct: 70  SGSTEPVCV-GDECEHARFFPQVQLNYADNLLGQAVAAPDTPALTACHADGRRVRLTRGE 128

Query: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180
           LR  V+RL  AL   G+  GDRV  +M N  + +   LA  ++GA  S+ + +   + +L
Sbjct: 129 LRNRVARLAHALSELGLRDGDRVVGVMRNDADAVVAALAVTALGATLSTAAAEMSVETIL 188

Query: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPTVIVPYAGDSAALAPTVEGG 240
           DRF  +AP+L               +   V  +A +L +   +V    D   L  TV+  
Sbjct: 189 DRFAPLAPRLLFAHVAEREFDTGMSLADNVADLAAALPSLQGVVRL--DDGTLPGTVKQR 246

Query: 241 V-TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFH 299
           + +L + I    AG  V+ R PF HPL+I+FSSGTTG PKCIVH AGG+LL+HLKEHR H
Sbjct: 247 IYSLGELIDSGDAGSFVWRRFPFNHPLFIMFSSGTTGKPKCIVHGAGGSLLEHLKEHRLH 306

Query: 300 CGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVF 359
           C LR G+RL++ TTC WMMWNW  S LA GA +  YDG     D   L+   A ER  VF
Sbjct: 307 CDLRPGDRLYFHTTCAWMMWNWQLSALASGAEIVTYDGPISTVD--ALWRLVADERVTVF 364

Query: 360 GTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGG 419
           GTS  Y+      G  P +  DL +LR M STG+ L    F +V + +KP + L SISGG
Sbjct: 365 GTSPAYLKMCEDAGLVPGQQFDLGALRAMMSTGAVLFDAQFEWVRDHVKP-LPLQSISGG 423

Query: 420 TDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMF 479
           TDI+ CFVLGNP  P++ GE Q   L L V  W       R   GELVC   FPS P+ F
Sbjct: 424 TDILGCFVLGNPNLPIYAGEAQCKSLALDVQAWEQGAHTSR--IGELVCANPFPSRPLGF 481

Query: 480 WNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQ 539
           + D DG  + AAYF R   VW HGD  E++P G   +HGRSD  LN  G+ +G  EIY  
Sbjct: 482 FGDMDGKGFHAAYFTRNPGVWTHGDRIEFSPEGTARLHGRSDGILNVRGINVGPGEIYRV 541

Query: 540 VEQMDEVAEALCIGQ-----------DWEDDVRVVLFVRLARGVELTEALTREIKNRIRS 588
           +  + ++ EAL + Q               D R+VL + L  GV LT AL   ++  +  
Sbjct: 542 LSDIRDIREALVVEQRSCAAPPDRTHAERYDQRIVLLLVLQDGVALTGALATRVRRDLAR 601

Query: 589 GASPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALD 640
            ASP HVP  IIAV ++P T +GK+ E A R+ ++G PV N  AL NP  LD
Sbjct: 602 RASPAHVPDLIIAVDELPVTHNGKLSEAAARNAINGLPVGNAAALRNPGCLD 653


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: 1868
Number of extensions: 106
Number of successful extensions: 8
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: 1020
Length adjustment: 41
Effective length of query: 609
Effective length of database: 979
Effective search space:   596211
Effective search space used:   596211
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: 56 (26.2 bits)

Align candidate RR42_RS10085 RR42_RS10085 (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.3095.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-182  592.9   0.0   4.6e-182  592.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS10085  RR42_RS10085 acetoacetyl-CoA syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS10085  RR42_RS10085 acetoacetyl-CoA synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.4   0.0  4.6e-182  4.6e-182       6     645 ..      11     656 ..       7     662 .. 0.93

  Alignments for each domain:
  == domain 1  score: 592.4 bits;  conditional E-value: 4.6e-182
                                 TIGR01217   6 lwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsd.vvfssaekevvdd 73 
                                               ++   +er + ++++ f  a    +G+ +gdyd l+++sv+e+ +fw+ ++++s+ +  s +++ v  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085  11 IYGSTSERAAASQMTAFTTALQAYTGQVFGDYDTLHDFSVREYRTFWQCFVQWSHgLAWSGSTEPVCVG 79 
                                               566678999********************************************8626778888889999 PP

                                 TIGR01217  74 skmlaarffpgarlnyaenllrkkgs...edallyvdeekesakvtfeelrrqvaslaaalralGvkkG 139
                                               ++   arffp+ +lnya+nll ++ +    +al     +    ++t  elr++va+la al +lG++ G
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085  80 DECEHARFFPQVQLNYADNLLGQAVAapdTPALTACHADGRRVRLTRGELRNRVARLAHALSELGLRDG 148
                                               *********************99877665677888888999**************************** PP

                                 TIGR01217 140 drvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrek 208
                                               drv+g++ n ++av+a la +++Ga  s+++ ++ ++++ldrf+ ++p+llf+  + +         ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 149 DRVVGVMRNDADAVVAALAVTALGATLSTAAAEMSVETILDRFAPLAPRLLFAHVAEREFDTGMSLADN 217
                                               ****************************************************99888888888999*** PP

                                 TIGR01217 209 vrevakelpdlravvlipyvgdreklapkvegal.tledllaaaqaaelvfeqlpfdhplyilfssGtt 276
                                               v+++a  lp+l+ vv +       +l  +v++ +  l +l+ + +a+  v+ + pf+hpl+i+fssGtt
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 218 VADLAAALPSLQGVVRLD----DGTLPGTVKQRIySLGELIDSGDAGSFVWRRFPFNHPLFIMFSSGTT 282
                                               **************9875....4455556665542799******************************* PP

                                 TIGR01217 277 GvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpat 345
                                               G pk+ivh aGG l++hlkeh+lhcdl++gdrl+++tt+ wmmwn+  s+la Ga +v ydG   + + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 283 GKPKCIVHGAGGSLLEHLKEHRLHCDLRPGDRLYFHTTCAWMMWNWQLSALASGAEIVTYDGP--ISTV 349
                                               **************************************************************5..6799 PP

                                 TIGR01217 346 nvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvll 414
                                               ++l++l++ e++tv+Gts +y+++++++gl p +++dl alr+++stG+ l    fe+v + +k+ + l
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 350 DALWRLVADERVTVFGTSPAYLKMCEDAGLVPGQQFDLGALRAMMSTGAVLFDAQFEWVRDHVKP-LPL 417
                                               ***************************************************************98.899 PP

                                 TIGR01217 415 asisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnd 483
                                                sisGGtdi+ cfv++np lp+y Ge q+++l l+v+aw++  ++     Gelv+++p+ps p+ f+ d
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 418 QSISGGTDILGCFVLGNPNLPIYAGEAQCKSLALDVQAWEQGAHT--SRIGELVCANPFPSRPLGFFGD 484
                                               ***************************************987665..679******************* PP

                                 TIGR01217 484 edGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslv 552
                                                dG  +++ayf + pgvw+hGd ie++p+G+  +hGrsd+ ln  G+ +G  eiy ++  + +++e+lv
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 485 MDGKGFHAAYFTRNPGVWTHGDRIEFSPEGTARLHGRSDGILNVRGINVGPGEIYRVLSDIRDIREALV 553
                                               ********************************************************************* PP

                                 TIGR01217 553 igqeq..........edgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtl 611
                                               + q            e  ++r+vl++ l  G+ l+ al  ++++ +   +sp hvp+ ii+v+++p t 
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 554 VEQRScaappdrthaERYDQRIVLLLVLQDGVALTGALATRVRRDLARRASPAHVPDLIIAVDELPVTH 622
                                               *9864222211111134589************************************************* PP

                                 TIGR01217 612 sGkkvevavkdvvaGkpvenkgalsnpealdlye 645
                                               +Gk  e a ++ ++G pv n  al np  ld  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS10085 623 NGKLSEAAARNAINGLPVGNAAALRNPGCLDSIQ 656
                                               ****************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (1020 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: 14.27
//
[ok]

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

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Protein sequences (fasta format)
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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