Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_21765 AO353_21765 acetoacetyl-CoA synthetase

Query= BRENDA::Q9Z3R3
         (650 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21765
          Length = 651

 Score =  681 bits (1756), Expect = 0.0
 Identities = 348/648 (53%), Positives = 446/648 (68%), Gaps = 9/648 (1%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
           LW P  E + ++ M  F  +  +R+  + ADY A H WS+ +R  FW A+ +  ++   +
Sbjct: 5   LWQPSAERIGKTRMDAFRRFSNQRYNLTLADYPALHQWSIDQREDFWQAIVDFFEIKFHQ 64

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
                L +G +M +A +FP A LNFAE+LLR+  +  A+I   E+     L++ EL   V
Sbjct: 65  PASTVLREGPQMPNAEWFPGATLNFAEHLLRRRDNAIAVIAIAENGQRESLSYRELAEHV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           + LQ++LRA G+G GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG  GV+DRFGQ
Sbjct: 125 AGLQKSLRAAGVGQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTHGVVDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK+ D  +KV  + + L +    +IVPYA   A +     +  V 
Sbjct: 185 IEPKVLITCAGYRYAGKKIDQTTKVNEILERLPSLQQLIIVPYARPQARVDDYKTQANVA 244

Query: 243 LAD--FIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
           L D  +  G + G   F  +PF HPLYIL+SSGTTGVPKCI+HS GG LLQH+KEH  H 
Sbjct: 245 LWDSFYRPGGEPG---FVAVPFAHPLYILYSSGTTGVPKCIIHSVGGVLLQHVKEHGLHV 301

Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
            L   +RLFY+TTCGWMMWNWL S LAVG+++ LYDGSPF P    L D   +E  +VFG
Sbjct: 302 DLGPDDRLFYYTTCGWMMWNWLVSALAVGSSVVLYDGSPFHPGPQRLIDLIDSEAISVFG 361

Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
           TS KY+  +      P  +HDL SL+ + STGS LSP+ + +VY  IK D+ L+S+SGGT
Sbjct: 362 TSPKYLATLESNEIQPRLSHDLGSLKALLSTGSALSPQSYDYVYREIKSDLCLSSMSGGT 421

Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
           DI+SCF+ GNP+ PV RGE+Q  GLG+AV+VWN+ G+PV GEKGELVCTR FP+MP+  W
Sbjct: 422 DIISCFLAGNPVLPVRRGEMQCKGLGMAVEVWNEAGQPVIGEKGELVCTRHFPAMPIGLW 481

Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
           NDP   K RA+YF +F  VW  GD+AE  P+G  +IHGRSDA LNPGGVRIGTAEIY QV
Sbjct: 482 NDPQQEKLRASYFSQFPGVWAQGDYAEQRPNGSWLIHGRSDAVLNPGGVRIGTAEIYRQV 541

Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600
           E++ +V +++ IGQ W+DDVRVVLFVRL  GV L E L +EI+  IR+  +PRHVPAKI+
Sbjct: 542 EKIHQVLDSVAIGQQWQDDVRVVLFVRLRDGVTLDEKLEQEIRQVIRANTTPRHVPAKIV 601

Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
           AV DIPRT SGK+VELAVR+VVHG+PVKN +ALANPEAL+ F    EL
Sbjct: 602 AVTDIPRTISGKVVELAVRNVVHGQPVKNTDALANPEALEQFRDRPEL 649


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: 1324
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: 651
Length adjustment: 38
Effective length of query: 612
Effective length of database: 613
Effective search space:   375156
Effective search space used:   375156
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 AO353_21765 AO353_21765 (acetoacetyl-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.4817.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     3e-270  883.8   0.0   3.4e-270  883.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765  AO353_21765 acetoacetyl-CoA synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765  AO353_21765 acetoacetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  883.6   0.0  3.4e-270  3.4e-270       4     650 ..       3     649 ..       1     651 [] 0.98

  Alignments for each domain:
  == domain 1  score: 883.6 bits;  conditional E-value: 3.4e-270
                                     TIGR01217   4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68 
                                                   +vlw+p aer+ ++r++ fr +  +r+ ++l+dy al++ws+d++++fw+a+++f+++ f+++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765   3 EVLWQPSAERIGKTRMDAFRRFSNQRYNLTLADYPALHQWSIDQREDFWQAIVDFFEIKFHQPAS 67 
                                                   58**************************************************************9 PP

                                     TIGR01217  69 evv.ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalr 132
                                                    v+ ++ +m++a++fpga+ln+ae+llr++++  a++ ++e+ +   +++ el + va l+++lr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765  68 TVLrEGPQMPNAEWFPGATLNFAEHLLRRRDNAIAVIAIAENGQRESLSYRELAEHVAGLQKSLR 132
                                                   99935689********************************************************* PP

                                     TIGR01217 133 alGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyv 197
                                                   a Gv++Gdrva+ +pn+ ++++ +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ gy+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 133 AAGVGQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTHGVVDRFGQIEPKVLITCAGYR 197
                                                   ***************************************************************** PP

                                     TIGR01217 198 ynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegal.tledllaaaqaaelvfeq 260
                                                   y Gk+ d++ kv+e+   lp+l++ +++py+ ++++++  k ++ +  ++ +      +e+ f  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 198 YAGKKIDQTTKVNEILERLPSLQQLIIVPYARPQARVDDyKTQANVaLWDSFYRP--GGEPGFVA 260
                                                   ***********************************99987666555157888877..99****** PP

                                     TIGR01217 261 lpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvs 325
                                                   +pf hplyil+ssGttGvpk+i+hs GG+l+qh+keh+lh dl++ drl+yytt+Gwmmwn+lvs
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 261 VPFAHPLYILYSSGTTGVPKCIIHSVGGVLLQHVKEHGLHVDLGPDDRLFYYTTCGWMMWNWLVS 325
                                                   ***************************************************************** PP

                                     TIGR01217 326 glatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlva 390
                                                   +la+G+++vlydGsp+ p ++ l dl++ e i+v+Gts ky+ +++ ++++p  +hdl +l++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 326 ALAVGSSVVLYDGSPFHPGPQRLIDLIDSEAISVFGTSPKYLATLESNEIQPRLSHDLGSLKALL 390
                                                   ***************************************************************** PP

                                     TIGR01217 391 stGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawde 455
                                                   stGs l+p++++yvy+eik+d+ l+s+sGGtdi+scf+ +np+lpv +Ge+q++glG+ave+w+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 391 STGSALSPQSYDYVYREIKSDLCLSSMSGGTDIISCFLAGNPVLPVRRGEMQCKGLGMAVEVWNE 455
                                                   ***************************************************************** PP

                                     TIGR01217 456 eGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGr 520
                                                    G+pv gekGelv+t+ +p+mp+ +wnd++  k r++yf+++pgvwa Gdy+e  p+G+ +ihGr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 456 AGQPVIGEKGELVCTRHFPAMPIGLWNDPQQEKLRASYFSQFPGVWAQGDYAEQRPNGSWLIHGR 520
                                                   ***************************************************************** PP

                                     TIGR01217 521 sdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585
                                                   sda lnp+Gvr+G+aeiy +ve++ +v +s+ igq+++d ++rvvlfv+l  G+tlde+l +ei+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 521 SDAVLNPGGVRIGTAEIYRQVEKIHQVLDSVAIGQQWQD-DVRVVLFVRLRDGVTLDEKLEQEIR 584
                                                   ***************************************.************************* PP

                                     TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650
                                                   + ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G+pv+n +al+npeal+ +++ +el
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 585 QVIRANTTPRHVPAKIVAVTDIPRTISGKVVELAVRNVVHGQPVKNTDALANPEALEQFRDRPEL 649
                                                   ************************************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (652 nodes)
Target sequences:                          1  (651 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 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 7.26
//
[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