Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate PfGW456L13_2872 Acetoacetyl-CoA synthetase (EC 6.2.1.16)
Query= BRENDA::Q9Z3R3
(650 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872
Length = 651
Score = 705 bits (1820), Expect = 0.0
Identities = 359/646 (55%), Positives = 440/646 (68%), Gaps = 5/646 (0%)
Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65
LW PD + + ++ M F + +R DY A H WS+ +R FW A+ + + E
Sbjct: 5 LWQPDAKRIGKTRMEAFRRFINQRHHLKIDDYPALHQWSIDQRPDFWQAIVDFFDIRFHE 64
Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
+ L++G RM A++FP A LNFAE+LL++ A+I GE+ LTW EL V
Sbjct: 65 QPDAVLLEGPRMPSAQWFPGATLNFAEHLLQRRDDAIAVIAVGENGQREHLTWAELAEQV 124
Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
+ Q L A G+G GDRVAA MPN +T+ MLAT S+GAIWS SPDFG QGV+DRFGQ
Sbjct: 125 AGFQNGLIAAGVGVGDRVAACMPNTWQTLVAMLATTSLGAIWSCSSPDFGTQGVVDRFGQ 184
Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPT-VEGGVT 242
I PK+ + C GY Y GK D +KV + + L + ++VPYA A + + VT
Sbjct: 185 IEPKVLVTCAGYRYAGKEIDQTAKVNEILQRLPSLQQLIVVPYARPQAHIEEFHTQANVT 244
Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
L D G F +PF HPLYIL+SSGTTGVPKCI+HS GG LLQH+KEH H L
Sbjct: 245 LWDDFYE-PGGEPDFVPVPFAHPLYILYSSGTTGVPKCIIHSTGGVLLQHVKEHGLHGDL 303
Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
GERLFY+TTCGWMMWNWL S LA G+++ LYDGSPF P+ L D ER +VFGTS
Sbjct: 304 GPGERLFYYTTCGWMMWNWLVSALATGSSVVLYDGSPFQPEPQRLIDLIDDERISVFGTS 363
Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
KY+ + G P +HDLSSL+ + TGS LSP + FVY K DV LAS+SGGTDI
Sbjct: 364 PKYLATLESSGIKPRESHDLSSLKTLLCTGSALSPHSYDFVYRDFKADVCLASMSGGTDI 423
Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
VSCFV GNP+ PV RGEI G LG+AV+VWNDEG PV GEKGELVCTR FP+MP+ WND
Sbjct: 424 VSCFVNGNPMSPVRRGEIMGKSLGMAVEVWNDEGHPVIGEKGELVCTRHFPAMPIGLWND 483
Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
PDG K R +YF F VW GD+AE PHGG++IHGRSDA LNPGGVRIGTAEIY QVE+
Sbjct: 484 PDGEKLRKSYFSLFPGVWAQGDYAEQLPHGGMMIHGRSDAVLNPGGVRIGTAEIYRQVEK 543
Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
+ +V + + IGQ W+DDVRVVLFVRL G+EL EAL ++I+ IR+ +PRHVPAKI+AV
Sbjct: 544 VPQVLDCVAIGQQWQDDVRVVLFVRLRDGLELDEALQQQIRQVIRANTTPRHVPAKIVAV 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: 1377
Number of extensions: 67
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 PfGW456L13_2872 (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.11673.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2e-275 900.9 0.0 2.2e-275 900.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 Acetoacetyl-CoA synthetase (EC 6
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 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 ! 900.8 0.0 2.2e-275 2.2e-275 5 650 .. 4 649 .. 1 651 [] 0.98
Alignments for each domain:
== domain 1 score: 900.8 bits; conditional E-value: 2.2e-275
TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefs 59
+lw+pda+r+ ++r++ fr ++ +r+ + + dy al++ws+d++ +fw+a+++f+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 4 ILWQPDAKRIGKTRMEAFRRFINQRHHLKIDDYPALHQWSIDQRPDFWQAIVDFF 58
79***************************************************** PP
TIGR01217 60 dvvfssaekev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesa 113
d++f+++ ++v +++ +m++a++fpga+ln+ae+ll++++ a++ v+e+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 59 DIRFHEQPDAVlLEGPRMPSAQWFPGATLNFAEHLLQRRDDAIAVIAVGENGQRE 113
***987766652799**************************************** PP
TIGR01217 114 kvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaallatasvGaiwss 168
++t++el +qva +++ l a Gv+ Gdrva+ +pn+ ++++a+lat+s+Gaiws
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 114 HLTWAELAEQVAGFQNGLIAAGVGVGDRVAACMPNTWQTLVAMLATTSLGAIWSC 168
******************************************************* PP
TIGR01217 169 cspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravv 223
+spdfG++gv+drf+qiepk+l+++ gy+y Gke d++ kv+e+ + lp+l++ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 169 SSPDFGTQGVVDRFGQIEPKVLVTCAGYRYAGKEIDQTAKVNEILQRLPSLQQLI 223
******************************************************* PP
TIGR01217 224 lipyvgdreklap..kvegaltledllaaaqaaelvfeqlpfdhplyilfssGtt 276
++py+ ++++++ + + ++d+ +e+ f +pf hplyil+ssGtt
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 224 VVPYARPQAHIEEfhTQANVTLWDDFYEP--GGEPDFVPVPFAHPLYILYSSGTT 276
*********99887455566679***998..99********************** PP
TIGR01217 277 GvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGa 331
Gvpk+i+hs+GG+l+qh+keh+lh+dl++g+rl+yytt+Gwmmwn+lvs+latG+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 277 GVPKCIIHSTGGVLLQHVKEHGLHGDLGPGERLFYYTTCGWMMWNWLVSALATGS 331
******************************************************* PP
TIGR01217 332 tlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsal 386
++vlydGsp+ p+++ l dl++ e+i+v+Gts ky+ +++ +g+kp ++hdls+l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 332 SVVLYDGSPFQPEPQRLIDLIDDERISVFGTSPKYLATLESSGIKPRESHDLSSL 386
******************************************************* PP
TIGR01217 387 rlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGei 441
++++ tGs l+p+++++vy+ +kadv las+sGGtdivscfv +np+ pv +Gei
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 387 KTLLCTGSALSPHSYDFVYRDFKADVCLASMSGGTDIVSCFVNGNPMSPVRRGEI 441
******************************************************* PP
TIGR01217 442 qapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdk 496
+++lG+ave+w++eG+pv gekGelv+t+ +p+mp+ +wnd+dG k rk+yf+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 442 MGKSLGMAVEVWNDEGHPVIGEKGELVCTRHFPAMPIGLWNDPDGEKLRKSYFSL 496
******************************************************* PP
TIGR01217 497 ypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveesl 551
+pgvwa Gdy+e p+Gg++ihGrsda lnp+Gvr+G+aeiy +ve++++v +++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 497 FPGVWAQGDYAEQLPHGGMMIHGRSDAVLNPGGVRIGTAEIYRQVEKVPQVLDCV 551
******************************************************* PP
TIGR01217 552 vigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievag 606
igq+++d ++rvvlfv+l G +ldeal ++i++ ira+ +prhvp+ki++v++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 552 AIGQQWQD-DVRVVLFVRLRDGLELDEALQQQIRQVIRANTTPRHVPAKIVAVTD 605
********.********************************************** PP
TIGR01217 607 iprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650
iprt+sGk ve+av++vv+G+ v+n +al+npeal+ +++ +el
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2872 606 IPRTISGKVVELAVRNVVHGQKVKNTDALANPEALEQFRDRPEL 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.68
//
[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