Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6.2.1.16)
Query= BRENDA::Q9Z3R3
(650 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042
Length = 651
Score = 687 bits (1774), Expect = 0.0
Identities = 355/647 (54%), Positives = 439/647 (67%), Gaps = 7/647 (1%)
Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
LW P E + +S M F + R DY A H WS+ +R AFW A+ + ++ +
Sbjct: 5 LWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQ 64
Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
+ + LV+G +M A++FP A LNFAE+LLR+ A++ E+ +LTW EL A V
Sbjct: 65 APDAVLVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHV 124
Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
+ LQ +L+A G+ GDRVAA MPN +T+ MLAT S+GAIWS SPDFG QGV+DRFGQ
Sbjct: 125 AGLQTSLKAAGVTQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQ 184
Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP--TVEGGV 241
I PK+ I C GY Y GK D +KV + + L + +++PYA A + T
Sbjct: 185 IEPKVLITCAGYRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDFKTPAAVA 244
Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
DF G F +PF HPLYIL+SSGTTGVPKCIVH GG LLQH+KEH H
Sbjct: 245 LWNDFYQS--GGEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVD 302
Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
L +RLFY+TTCGWMMWNWL S LAVG+T+ LYDGSPF P L D +R +VFGT
Sbjct: 303 LGPEDRLFYYTTCGWMMWNWLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGT 362
Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
S K++ A+ G P +TH L SLR + STGS L+P + +VY IK DV LAS+SGGTD
Sbjct: 363 SPKFLAALESEGLKPRQTHRLDSLRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTD 422
Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
IVSCFV GNPL PV RGE+QG LG+AV VWN+ G PV GEKGELVCTR FP+MP+ WN
Sbjct: 423 IVSCFVNGNPLSPVSRGEMQGKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWN 482
Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
DP K RA+YF +F VW GD+AE PHGG +IHGRSDA LNPGGVRIGTAEIY QVE
Sbjct: 483 DPRQEKLRASYFAQFPGVWAQGDYAEELPHGGFLIHGRSDAVLNPGGVRIGTAEIYRQVE 542
Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
++++V + + IGQ W+ DVRVVLFVRL GV L EAL ++I+ IR+ +PRHVPAKI+A
Sbjct: 543 KVEQVLDCVAIGQRWQGDVRVVLFVRLRDGVTLNEALAQQIRQVIRANTTPRHVPAKILA 602
Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
V+DIPRT SGK+VELAVR+VVHG VKN +ALANPEAL+ F EL
Sbjct: 603 VSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEALEQFRDRPEL 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: 1361
Number of extensions: 70
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 Pf6N2E2_2042 (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.22748.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-271 886.9 0.0 3.8e-271 886.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 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 ! 886.8 0.0 3.8e-271 3.8e-271 5 650 .. 4 649 .. 1 651 [] 0.98
Alignments for each domain:
== domain 1 score: 886.8 bits; conditional E-value: 3.8e-271
TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68
+lw+p er++++r++ fr++v r+ + l dy al+ ws+d+++afw+a+++f+++ f++a +
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 4 ILWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQAPD 67
79********************************************************998777 PP
TIGR01217 69 ev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaal 131
+v v++ +m++a++fpga+ln+ae+llr+++ a++ de+ + ++t++el + va l+++l
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 68 AVlVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHVAGLQTSL 131
652899********************************************************** PP
TIGR01217 132 ralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdg 195
+a Gv +Gdrva+ +pn+ ++++ +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ g
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 132 KAAGVTQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQIEPKVLITCAG 195
**************************************************************** PP
TIGR01217 196 yvynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegalt.ledllaaaqaaelv 257
y+y Gk d+r kv+e+ lp+l++ +++py+ + + ++ k ++a+ ++d+ + +e+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 196 YRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDfKTPAAVAlWNDFYQS--GGEPA 257
**********************************998766559999986489**999..99*** PP
TIGR01217 258 feqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwn 321
f +pfdhplyil+ssGttGvpk+ivh +GG+l+qh+keh+lh dl++ drl+yytt+Gwmmwn
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 258 FVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVDLGPEDRLFYYTTCGWMMWN 321
**************************************************************** PP
TIGR01217 322 flvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsa 385
+lvs+la+G+t+vlydGsp+ p ++ l dl+++++i+v+Gts k++ a++ +glkp +th l++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 322 WLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGTSPKFLAALESEGLKPRQTHRLDS 385
**************************************************************** PP
TIGR01217 386 lrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGla 449
lr+++stGs l p++++yvy+ ikadv las+sGGtdivscfv +np+ pv +Ge+q+++lG+a
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 386 LRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTDIVSCFVNGNPLSPVSRGEMQGKSLGMA 449
**************************************************************** PP
TIGR01217 450 veawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513
v++w+e G+pv gekGelv+t+ +p+mp+ +wnd+ k r++yf ++pgvwa Gdy+e p+G
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 450 VQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWNDPRQEKLRASYFAQFPGVWAQGDYAEELPHG 513
**************************************************************** PP
TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatld 577
g +ihGrsda lnp+Gvr+G+aeiy +ve++++v +++ igq ++ g++rvvlfv+l G+tl+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 514 GFLIHGRSDAVLNPGGVRIGTAEIYRQVEKVEQVLDCVAIGQRWQ-GDVRVVLFVRLRDGVTLN 576
*******************************************98.5***************** PP
TIGR01217 578 ealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpeal 641
eal ++i++ ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G++v+n +al+npeal
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 577 EALAQQIRQVIRANTTPRHVPAKILAVSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEAL 640
**************************************************************** PP
TIGR01217 642 dlyeeleel 650
+ +++ +el
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 641 EQFRDRPEL 649
****98887 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: 11.31
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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