Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO356_00425 AO356_00425 acetoacetyl-CoA synthetase
Query= BRENDA::Q9Z3R3
(650 letters)
>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 AO356_00425
acetoacetyl-CoA synthetase
Length = 651
Score = 686 bits (1769), Expect = 0.0
Identities = 353/649 (54%), Positives = 442/649 (68%), Gaps = 7/649 (1%)
Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
LW P E + +S M F + R DY H WS+ +R AFW A+ + ++
Sbjct: 5 LWQPSPERIAQSRMNAFRRFVNARHHLQLNDYPTLHAWSIDQREAFWQAIVDFFEIRFHH 64
Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
+ + LV+G +M A++FP A LNFAE+LLR+ A++ GE+ +LTW EL A V
Sbjct: 65 APDAVLVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALGENGGQEQLTWAELAAHV 124
Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
+ LQ++L+A G+ GDRVAA MPN +T+ MLA+ S+GAIWS SPDFG QGV+DRFGQ
Sbjct: 125 AGLQKSLQAAGVTRGDRVAACMPNTWQTLVGMLASTSLGAIWSCSSPDFGTQGVIDRFGQ 184
Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP--TVEGGV 241
I PK+ I C GY Y GK D +KV + + L + +++PYA A L T
Sbjct: 185 IEPKVLITCAGYRYAGKVIDQRAKVNEILERLPSLQQLIVLPYAQPDARLEDFKTPAAIA 244
Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301
DF + G F +PF HPLYIL+SSGTTGVPKCIVH GG LLQH+KEH H
Sbjct: 245 LWNDFYQ--RGGEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVD 302
Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361
L +RLFY+TTCGWMMWNWL S LAVG+ + LYDGSPF P L D +R +VFGT
Sbjct: 303 LGPEDRLFYYTTCGWMMWNWLVSALAVGSAVVLYDGSPFHPGPERLLDLIDQQRISVFGT 362
Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421
S K++ A+ G P +TH L SL+ + STGS L+P + +VY +KPDV LAS+SGGTD
Sbjct: 363 SPKFLAALESEGLKPRQTHRLDSLKTLLSTGSALAPHSYDYVYRDVKPDVCLASMSGGTD 422
Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481
IVSCFV GNPL PV RGE+QG LG+AV VWN+ G PV GEKGELVCTR FP+MP+ WN
Sbjct: 423 IVSCFVNGNPLSPVRRGEMQGKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWN 482
Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
DP K RA+YF +F VW GD+AE PHGG++IHGRSDA LNPGGVRIGTAEIY QVE
Sbjct: 483 DPRQEKLRASYFAQFPGVWAQGDYAEELPHGGLLIHGRSDAVLNPGGVRIGTAEIYRQVE 542
Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
++++V +++ IGQ W+ DVRVVLFVRL GV L +AL + I+ IR+ +PRHVPAKI+A
Sbjct: 543 KVEQVLDSIAIGQQWQGDVRVVLFVRLRDGVTLDQALEQRIRQVIRTHTTPRHVPAKILA 602
Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
V+DIPRT SGK+VELAVR+VVHG VKN +ALANPEAL+ F EL S
Sbjct: 603 VSDIPRTISGKVVELAVRNVVHGEVVKNTDALANPEALEQFRDRPELAS 651
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: 1380
Number of extensions: 72
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 AO356_00425 AO356_00425 (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.6117.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.3e-268 877.6 0.0 2.5e-268 877.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 AO356_00425 acetoacetyl-CoA synt
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 AO356_00425 acetoacetyl-CoA synthetase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 877.5 0.0 2.5e-268 2.5e-268 5 650 .. 4 649 .. 1 651 [] 0.98
Alignments for each domain:
== domain 1 score: 877.5 bits; conditional E-value: 2.5e-268
TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssae 67
lw+p er++++r++ fr +v r+ + l dy l+ ws+d+++afw+a+++f++++f++a
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 4 LLWQPSPERIAQSRMNAFRRFVNARHHLQLNDYPTLHAWSIDQREAFWQAIVDFFEIRFHHAP 66
69*********************************************************9877 PP
TIGR01217 68 kev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaa 129
++v v++ +m++a++fpga+ln+ae+llr+++ a++ +e+ + ++t++el + va l++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 67 DAVlVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALGENGGQEQLTWAELAAHVAGLQK 129
7652899******************************************************** PP
TIGR01217 130 alralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfs 192
+l+a Gv +Gdrva+ +pn+ ++++ +la++s+Gaiws +spdfG++gv+drf+qiepk+l++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 130 SLQAAGVTRGDRVAACMPNTWQTLVGMLASTSLGAIWSCSSPDFGTQGVIDRFGQIEPKVLIT 192
*************************************************************** PP
TIGR01217 193 vdgyvynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegalt.ledllaaaqa 253
+ gy+y Gk d+r kv+e+ lp+l++ +++py+ + ++l+ k ++a+ ++d+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 193 CAGYRYAGKVIDQRAKVNEILERLPSLQQLIVLPYAQPDARLEDfKTPAAIAlWNDFYQR--G 253
*************************************99987666999998637999876..9 PP
TIGR01217 254 aelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvG 316
+e+ f +pfdhplyil+ssGttGvpk+ivh +GG+l+qh+keh+lh dl++ drl+yytt+G
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 254 GEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVDLGPEDRLFYYTTCG 316
9************************************************************** PP
TIGR01217 317 wmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkpar 379
wmmwn+lvs+la+G+++vlydGsp+ p ++ l dl+++++i+v+Gts k++ a++ +glkp +
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 317 WMMWNWLVSALAVGSAVVLYDGSPFHPGPERLLDLIDQQRISVFGTSPKFLAALESEGLKPRQ 379
*************************************************************** PP
TIGR01217 380 thdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiq 442
th l++l++++stGs l p++++yvy+ +k+dv las+sGGtdivscfv +np+ pv +Ge+q
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 380 THRLDSLKTLLSTGSALAPHSYDYVYRDVKPDVCLASMSGGTDIVSCFVNGNPLSPVRRGEMQ 442
*************************************************************** PP
TIGR01217 443 apglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGd 505
+++lG+av++w+e G+pv gekGelv+t+ +p+mp+ +wnd+ k r++yf ++pgvwa Gd
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 443 GKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWNDPRQEKLRASYFAQFPGVWAQGD 505
*************************************************************** PP
TIGR01217 506 yieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfv 568
y+e p+Gg++ihGrsda lnp+Gvr+G+aeiy +ve++++v +s+ igq+++ g++rvvlfv
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 506 YAEELPHGGLLIHGRSDAVLNPGGVRIGTAEIYRQVEKVEQVLDSIAIGQQWQ-GDVRVVLFV 567
***************************************************98.5******** PP
TIGR01217 569 klasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpven 631
+l G+tld+al ++i++ ir+ +prhvp+ki++v++iprt+sGk ve+av++vv+G+ v+n
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 568 RLRDGVTLDQALEQRIRQVIRTHTTPRHVPAKILAVSDIPRTISGKVVELAVRNVVHGEVVKN 630
*************************************************************** PP
TIGR01217 632 kgalsnpealdlyeeleel 650
+al+npeal+ +++ +el
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00425 631 TDALANPEALEQFRDRPEL 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 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 8.14
//
[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