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)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5634
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.13317.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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.30
//
[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:
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