GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Acidovorax sp. GW101-3H11

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Ac3H11_4867 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::D6EQU8
         (658 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4867
          Length = 710

 Score =  610 bits (1572), Expect = e-179
 Identities = 324/692 (46%), Positives = 427/692 (61%), Gaps = 49/692 (7%)

Query: 8   PLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRF 67
           P   P    I Q R+  +Q W  +  G   +  Y AL RWS  ELD FW++V ++F +  
Sbjct: 21  PATGPQPPYIPQIRL--YQNWLRDERGLQWDS-YDALWRWSTTELDAFWQSVWDYFQIES 77

Query: 68  STPYARVLGDRTMPGAQWFPGATLNYAEHALRA--AGTRPDEPALLYVDETHEPAPVTWA 125
            TP+  VLG  TMPGAQWFPGA +NYA  ALR   A      PA++  +E  +   ++W 
Sbjct: 78  PTPHTAVLGKNTMPGAQWFPGAQVNYARQALRHVDAAHAAGLPAIISRNEKGQHRELSWP 137

Query: 126 ELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSV 185
           ELRRQVASLA  L+A GV PGDRV+ YLPN+P+A++A LAT ++GGVW+ CAPD G  +V
Sbjct: 138 ELRRQVASLALHLKAQGVMPGDRVAAYLPNVPEAMIAFLATVSIGGVWSICAPDMGTHAV 197

Query: 186 LDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGT-EAPDGTL 244
           LDRF+Q+ P VL  VDG  YGG++HDRR  +AELR  LP+++   H  LLG  +A     
Sbjct: 198 LDRFRQIAPKVLIGVDGVSYGGRDHDRRPVLAELREALPSVQ---HAVLLGNLDASVSIA 254

Query: 245 DWETLTAADA---------EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295
            W + T A A         EP++  +PFDHPLW++YSSGTTGLPK IV   GG ++  L+
Sbjct: 255 GWASWTGATARSDAETTAFEPLW--LPFDHPLWIVYSSGTTGLPKPIVHGHGGTVLVALQ 312

Query: 296 QLGLHCDLGP-------GDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGF----PA 344
              LH D+G        G+R+ WY+STGW+MWN  +SGLL+GTT V+YDG+PG     P 
Sbjct: 313 LKVLHNDIGCSYEPNSFGERYHWYSSTGWVMWNAQLSGLLSGTTCVIYDGNPGGSKDNPD 372

Query: 345 TDAQWRIAERTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWL 404
               WR A  TG T FG  AA+   C KAG+  A   DL+ I+ + TTGSPL P+   W 
Sbjct: 373 WGVLWRFAAETGVTFFGAGAAFFANCMKAGITLADYGDLTRIRALGTTGSPLSPEVQEWG 432

Query: 405 HDEFAA-GGADLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPL 463
             +F A G +D+W  ++SGGTD C  F G    +P   GE+Q   LG  ++SWD  G P+
Sbjct: 433 TAQFEALGTSDIWWNNISGGTDFCGAFIGGHREMPQVPGEMQCRMLGAAVESWDAEGRPV 492

Query: 464 TDEVGELVVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPG-----------------VWRH 506
            D VGELV   P+PSMP+  W D DGSRY  SYFD YP                  VWRH
Sbjct: 493 QDAVGELVCAQPIPSMPLYLWGDKDGSRYLSSYFDMYPAGHGRQPGGGDGPAAMGAVWRH 552

Query: 507 GDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYW 566
           GDW+ + + G  VI+GRSD+T+NR G+RMG+++IY AVE LPE+ +SLV+ +E      +
Sbjct: 553 GDWLKIGANGGCVIYGRSDATINRHGLRMGTSEIYSAVESLPEVLDSLVVDLEYLGRESY 612

Query: 567 MPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRL 626
           MPLFV L PG  LDDAL  RI   +R  LSPR VPD++  V  +P TL+GK+ E+P+K+L
Sbjct: 613 MPLFVVLRPGYALDDALRARINGAVRTALSPRFVPDDIFAVAEVPRTLSGKKQELPIKKL 672

Query: 627 LQGTPLDKAVNPGSIDNLDLLHFYEELARKRS 658
           L G P++K VN  ++ N   L +Y   A +R+
Sbjct: 673 LLGQPIEKVVNKDAMANPGCLDWYVAFAAERA 704


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: 1701
Number of extensions: 111
Number of successful extensions: 7
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: 710
Length adjustment: 39
Effective length of query: 619
Effective length of database: 671
Effective search space:   415349
Effective search space used:   415349
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 Ac3H11_4867 (Acetoacetyl-CoA synthetase (EC 6.2.1.16))
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.2924.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.2e-208  680.2   0.0   3.2e-208  678.9   0.0    1.5  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867  Acetoacetyl-CoA synthetase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867  Acetoacetyl-CoA synthetase (EC 6.2.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.9   0.0  3.2e-208  3.2e-208      18     648 ..      32     700 ..      29     704 .. 0.94

  Alignments for each domain:
  == domain 1  score: 678.9 bits;  conditional E-value: 3.2e-208
                                        TIGR01217  18 rlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskmlaa 79 
                                                      ++  ++++  ++ G+    ydal+rws +eldafw++vw+++++   +++ +v+++++m++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867  32 QIRLYQNWLRDERGLQWDSYDALWRWSTTELDAFWQSVWDYFQIESPTPHTAVLGKNTMPGA 93 
                                                      577799******************************************************** PP

                                        TIGR01217  80 rffpgarlnyaenllrkkgs.....edallyvdeekesakvtfeelrrqvaslaaalralGv 136
                                                      ++fpga++nya ++lr+ ++      +a++ ++e+ +  ++++ elrrqvasla  l+a+Gv
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867  94 QWFPGAQVNYARQALRHVDAahaagLPAIISRNEKGQHRELSWPELRRQVASLALHLKAQGV 155
                                                      *****************998655555678999999999************************ PP

                                        TIGR01217 137 kkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvy 198
                                                       +Gdrva+ylpn+pea+ a+lat s+G++ws c+pd+G+++vldrf qi+pk+l+ vdg+ y
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 156 MPGDRVAAYLPNVPEAMIAFLATVSIGGVWSICAPDMGTHAVLDRFRQIAPKVLIGVDGVSY 217
                                                      ************************************************************** PP

                                        TIGR01217 199 nGkehdrrekvrevakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeq 260
                                                      +G++hdrr  ++e++  lp++++ vl+  +      ++ + g   +   +a  +a    fe 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 218 GGRDHDRRPVLAELREALPSVQHAVLLGNLD----ASVSIAGWASWTGATARSDAETTAFEP 275
                                                      *******************999999988777....3445688999******9999999**96 PP

                                        TIGR01217 261 ..lpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltd.......gdrllyyt 313
                                                        lpfdhpl+i++ssGttG+pk ivh  GGt++  l+ +vlh d++        g+r+ +y+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 276 lwLPFDHPLWIVYSSGTTGLPKPIVHGHGGTVLVALQLKVLHNDIGCsyepnsfGERYHWYS 337
                                                      337***************************************99974223334479****** PP

                                        TIGR01217 314 tvGwmmwnflvsglatGatlvlydGspl....vpatnvlfdlaeregitvlGtsakyvsavr 371
                                                      ++Gw+mwn   sgl+ G+t v+ydG p+     p+  vl+++a+ +g+t +G++a++   + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 338 STGWVMWNAQLSGLLSGTTCVIYDGNPGgskdNPDWGVLWRFAAETGVTFFGAGAAFFANCM 399
                                                      *************************997333358888************************* PP

                                        TIGR01217 372 kkglkparthdlsalrlvastGsplkpegfeyvyeeika....dvllasisGGtdivscfvg 429
                                                      k+g++ a   dl+ +r++ +tGspl+pe  e+   +++a    d++   isGGtd +  f+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 400 KAGITLADYGDLTRIRALGTTGSPLSPEVQEWGTAQFEAlgtsDIWWNNISGGTDFCGAFIG 461
                                                      ********************************99999888888******************* PP

                                        TIGR01217 430 anpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrk 491
                                                      +   +p   Ge+q++ lG ave+wd eG+pv++++Gelv+++p+psmp+ +w d+dGs+y +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 462 GHREMPQVPGEMQCRMLGAAVESWDAEGRPVQDAVGELVCAQPIPSMPLYLWGDKDGSRYLS 523
                                                      ************************************************************** PP

                                        TIGR01217 492 ayfdkyp.......g..........vwahGdyieltprGgivihGrsdatlnpnGvrlGsae 536
                                                      +yfd yp       g          vw+hGd+ ++ ++Gg vi+Grsdat+n++G+r+G++e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 524 SYFDMYPaghgrqpGggdgpaamgaVWRHGDWLKIGANGGCVIYGRSDATINRHGLRMGTSE 585
                                                      ******8555444404455555556************************************* PP

                                        TIGR01217 537 iynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvp 598
                                                      iy ave l+ev +slv+  e    e +++lfv l +G  ld+al  +i+ a+r++lspr vp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 586 IYSAVESLPEVLDSLVVDLEYLGRESYMPLFVVLRPGYALDDALRARINGAVRTALSPRFVP 647
                                                      ************************************************************** PP

                                        TIGR01217 599 skiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdlyeele 648
                                                      + i +va++prtlsGkk e+++k+++ G+p+e   nk+a++np  ld y  ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 648 DDIFAVAEVPRTLSGKKQELPIKKLLLGQPIEkvvNKDAMANPGCLDWYVAFA 700
                                                      *******************************9999**************8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (710 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 5.67
//
[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:

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