GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N1B4

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_5634 Acetoacetyl-CoA synthetase (EC 6.2.1.16)

Query= BRENDA::Q9Z3R3
         (650 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 Acetoacetyl-CoA
           synthetase (EC 6.2.1.16)
          Length = 651

 Score =  702 bits (1812), Expect = 0.0
 Identities = 357/646 (55%), Positives = 443/646 (68%), Gaps = 5/646 (0%)

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

Query: 66  SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
             +  L++G +M  A++FP A LNFAE+LLR+     A++  GE+    +LTW EL + V
Sbjct: 65  QPDAVLIEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVAIGENGQREQLTWAELASHV 124

Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
           +  Q  L+A G+G GDRVAA MPN  +T+  MLAT S+GAIWS  SPDFG  GV+DRFGQ
Sbjct: 125 AGFQNGLKAAGVGLGDRVAACMPNTWQTLVAMLATTSLGAIWSCSSPDFGTHGVIDRFGQ 184

Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242
           I PK+ I C GY Y GK  D  +KV  +   L +    ++VPYA   A +     +  VT
Sbjct: 185 IEPKVLITCAGYRYAGKEIDQTAKVNEILGQLPSLQQLIVVPYARPQARIEDFRSQANVT 244

Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
           L D       G   F  +PF HPLYIL+SSGTTGVPKCIVHS GG LLQH+KEH  H  L
Sbjct: 245 LWDDFYD-PGGEPQFIPVPFAHPLYILYSSGTTGVPKCIVHSTGGVLLQHVKEHGLHTDL 303

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
             G+RLFY+TTCGWMMWNWL S LAV + + LYDGSPF P    L D    ER  VFGTS
Sbjct: 304 GPGDRLFYYTTCGWMMWNWLVSALAVDSAVVLYDGSPFHPGPERLIDLIDDERINVFGTS 363

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
            K++ A+   G  P  +HDLSSL+ + STGS LSP+ F +VY   K D+ L+S+SGGTDI
Sbjct: 364 PKFLTALESNGLKPCDSHDLSSLKTVLSTGSALSPQSFDYVYRAFKSDLCLSSMSGGTDI 423

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           VSCFV+GNP+ PV RGE+Q  GLG+AV+VWND G PV GEKGELVCTR FP+MP+  W+D
Sbjct: 424 VSCFVIGNPVLPVRRGEMQCKGLGMAVEVWNDAGTPVIGEKGELVCTRHFPAMPIGLWHD 483

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
           PDG K R +YF  F  VW  GD+AE  PHGG++IHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 484 PDGEKLRKSYFSLFPGVWAQGDYAEQLPHGGLLIHGRSDAVLNPGGVRIGTAEIYRQVEK 543

Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
           + +V +++ IGQ W+DDVRVVLFV+L  GVEL EAL ++I+  IR+  +PRHVPAKI+AV
Sbjct: 544 IPQVLDSVAIGQQWQDDVRVVLFVKLRDGVELDEALQQQIRQVIRANTTPRHVPAKIVAV 603

Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
            DIPRT SGK+VELAVR+VVHG+ VKN +ALANPEAL+ F    EL
Sbjct: 604 TDIPRTISGKVVELAVRNVVHGQKVKNTDALANPEALEQFRDRPEL 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: 1363
Number of extensions: 63
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 Pf1N1B4_5634 (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.16829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.6e-274  897.9   0.0   1.8e-274  897.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634  Acetoacetyl-CoA synthetase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634  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 !  897.8   0.0  1.8e-274  1.8e-274       5     651 ..       4     650 ..       1     651 [] 0.98

  Alignments for each domain:
  == domain 1  score: 897.8 bits;  conditional E-value: 1.8e-274
                                      TIGR01217   5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68 
                                                    +lw+p +er+ ++r++ fr  + +r+ + ++dy al++ws+d+++afw+a+++f+d++f+ + +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634   4 ILWQPGTERIGKSRMEAFRRSINQRHNLKIADYPALHQWSIDQREAFWQAIVDFFDIRFHDQPD 67 
                                                    79********************************************************987766 PP

                                      TIGR01217  69 ev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaal 131
                                                    +v +++ +m++a++fpga+ln+ae+llr+++   a++ ++e+ +  ++t++el   va +++ l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634  68 AVlIEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVAIGENGQREQLTWAELASHVAGFQNGL 131
                                                    652799********************************************************** PP

                                      TIGR01217 132 ralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdg 195
                                                    +a Gv+ Gdrva+ +pn+ ++++a+lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 132 KAAGVGLGDRVAACMPNTWQTLVAMLATTSLGAIWSCSSPDFGTHGVIDRFGQIEPKVLITCAG 195
                                                    **************************************************************** PP

                                      TIGR01217 196 yvynGkehdrrekvrevakelpdlravvlipyvgdreklap.kve.galtledllaaaqaaelv 257
                                                    y+y Gke d++ kv+e+  +lp+l++ +++py+ ++++++  + + +   ++d+      +e++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 196 YRYAGKEIDQTAKVNEILGQLPSLQQLIVVPYARPQARIEDfRSQaNVTLWDDFYDP--GGEPQ 257
                                                    ************************************9988765551555699**998..99*** PP

                                      TIGR01217 258 feqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwn 321
                                                    f  +pf hplyil+ssGttGvpk+ivhs+GG+l+qh+keh+lh+dl++gdrl+yytt+Gwmmwn
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 258 FIPVPFAHPLYILYSSGTTGVPKCIVHSTGGVLLQHVKEHGLHTDLGPGDRLFYYTTCGWMMWN 321
                                                    **************************************************************** PP

                                      TIGR01217 322 flvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsa 385
                                                    +lvs+la+ +++vlydGsp+ p ++ l dl++ e+i v+Gts k+++a++ +glkp  +hdls+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 322 WLVSALAVDSAVVLYDGSPFHPGPERLIDLIDDERINVFGTSPKFLTALESNGLKPCDSHDLSS 385
                                                    **************************************************************** PP

                                      TIGR01217 386 lrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGla 449
                                                    l++v+stGs l+p++f+yvy+++k+d+ l+s+sGGtdivscfv +np+lpv +Ge+q++glG+a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 386 LKTVLSTGSALSPQSFDYVYRAFKSDLCLSSMSGGTDIVSCFVIGNPVLPVRRGEMQCKGLGMA 449
                                                    **************************************************************** PP

                                      TIGR01217 450 veawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
                                                    ve+w++ G pv gekGelv+t+ +p+mp+ +w d+dG k rk+yf+ +pgvwa Gdy+e  p+G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 450 VEVWNDAGTPVIGEKGELVCTRHFPAMPIGLWHDPDGEKLRKSYFSLFPGVWAQGDYAEQLPHG 513
                                                    **************************************************************** PP

                                      TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatld 577
                                                    g++ihGrsda lnp+Gvr+G+aeiy +ve++++v +s+ igq+++d ++rvvlfvkl  G++ld
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 514 GLLIHGRSDAVLNPGGVRIGTAEIYRQVEKIPQVLDSVAIGQQWQD-DVRVVLFVKLRDGVELD 576
                                                    **********************************************.***************** PP

                                      TIGR01217 578 ealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpeal 641
                                                    eal ++i++ ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G+ v+n +al+npeal
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 577 EALQQQIRQVIRANTTPRHVPAKIVAVTDIPRTISGKVVELAVRNVVHGQKVKNTDALANPEAL 640
                                                    **************************************************************** PP

                                      TIGR01217 642 dlyeeleelk 651
                                                    + +++ +el+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634 641 EQFRDRPELN 650
                                                    *****99886 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.78
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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