Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate YP_004141620.1 Mesci_2424 acetoacetate-CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000185905.1:YP_004141620.1
Length = 652
Score = 950 bits (2455), Expect = 0.0
Identities = 446/650 (68%), Positives = 527/650 (81%), Gaps = 2/650 (0%)
Query: 1 MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60
M AE+PLW P ++ ++ +P+ F G + G +F+ Y H WSV +R FW+ VW+ C
Sbjct: 1 MAAEQPLWTPTQDQIDAAPLTAFTKTAGVKAGVAFSSYSQLHAWSVEDREGFWSLVWDFC 60
Query: 61 KVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDE 120
++G+ G+K LVDGD+M A FFP+A LNFA NLL+KTGSGDA++FRGEDKV RL+W+E
Sbjct: 61 GIVGDKGDKLLVDGDKMPGASFFPDATLNFAGNLLKKTGSGDAIVFRGEDKVERRLSWNE 120
Query: 121 LRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVL 180
L AL SRLQQ + + GDR+AAMMPNMPET+A MLA AS+GA+WSSCSPDFGEQGVL
Sbjct: 121 LHALTSRLQQLFLSLKVKKGDRIAAMMPNMPETVAAMLAAASIGAVWSSCSPDFGEQGVL 180
Query: 181 DRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVE 238
DRFGQI P +FI DGYWYNGK +V K+ AVA LG ++V Y G S+ +A ++
Sbjct: 181 DRFGQIEPVVFIAPDGYWYNGKAIEVADKIAAVAAKLGTVHKILVVDYLGTSSDVAGIID 240
Query: 239 GGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRF 298
V L + ++ F P+ FE LPF HPLYILFSSGTTG+PKCIVHSAGGTL+QH+KEHR
Sbjct: 241 KAVALEEALSPFAGKPVAFEPLPFSHPLYILFSSGTTGIPKCIVHSAGGTLIQHVKEHRL 300
Query: 299 HCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAV 358
H GL DG+R FYFTTCGWMMWNWL SGLA GATL LYDGSPF PDGNVLFD+A AE+
Sbjct: 301 HAGLTDGDRFFYFTTCGWMMWNWLVSGLASGATLLLYDGSPFYPDGNVLFDFADAEKMTF 360
Query: 359 FGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISG 418
GTSAK+ID+VRK G P RTHDLS++R ++STGSPLSPE F FVY+GIK DV LAS+SG
Sbjct: 361 LGTSAKFIDSVRKAGLKPIRTHDLSTVRAISSTGSPLSPEDFRFVYDGIKKDVHLASVSG 420
Query: 419 GTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVM 478
GTDIVSCFVLG P +PVW GEIQGPGLGLAVDVW+D+G+PVR EKGELVC +AFP+MP+
Sbjct: 421 GTDIVSCFVLGVPTQPVWTGEIQGPGLGLAVDVWDDDGRPVRQEKGELVCAKAFPAMPIG 480
Query: 479 FWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYN 538
FWNDPDG KYRAAYF+RFDNVWCHGDFAEWT HGG++IHGRSDATLNPGGVRIGTAEIYN
Sbjct: 481 FWNDPDGKKYRAAYFERFDNVWCHGDFAEWTEHGGLIIHGRSDATLNPGGVRIGTAEIYN 540
Query: 539 QVEQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAK 598
QVEQM E+ EALCIGQD+++DVRV+LFVRLA GV+L E L + I+ +IRSGASPRHVPA+
Sbjct: 541 QVEQMPEILEALCIGQDFDNDVRVILFVRLAAGVQLDEDLEKRIRAKIRSGASPRHVPAR 600
Query: 599 IIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
I+AV DIPRTKSGKI ELAVRDVVHGR +KNKEALANPEAL+LF L +L
Sbjct: 601 IVAVTDIPRTKSGKITELAVRDVVHGRAIKNKEALANPEALELFKNLPQL 650
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: 1536
Number of extensions: 58
Number of successful extensions: 2
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: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space: 375768
Effective search space used: 375768
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 YP_004141620.1 Mesci_2424 (acetoacetate-CoA ligase)
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.29049.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1011.5 0.0 0 1011.3 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004141620.1 Mesci_2424 acetoacetate-CoA liga
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004141620.1 Mesci_2424 acetoacetate-CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1011.3 0.0 0 0 3 650 .. 4 650 .. 2 652 .] 0.99
Alignments for each domain:
== domain 1 score: 1011.3 bits; conditional E-value: 0
TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevv 71
eq+lw+p +++++ a+l+ f + +g + G a++ y +l+ wsv++++ fw+ vw+f+++v++++ k +v
lcl|NCBI__GCF_000185905.1:YP_004141620.1 4 EQPLWTPTQDQIDAAPLTAFTKTAGVKAGVAFSSYSQLHAWSVEDREGFWSLVWDFCGIVGDKGDKLLV 72
79******************************************************************* PP
TIGR01217 72 ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
d++km++a ffp+a+ln+a nll+k+gs+da+++++e+k+ +++++el ++ ++l++ + +l vkkGd
lcl|NCBI__GCF_000185905.1:YP_004141620.1 73 DGDKMPGASFFPDATLNFAGNLLKKTGSGDAIVFRGEDKVERRLSWNELHALTSRLQQLFLSLKVKKGD 141
********************************************************************* PP
TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
r+a+++pn+pe+vaa+la+as+Ga+wsscspdfG++gvldrf+qiep+++++ dgy+ynGk ++ +k+
lcl|NCBI__GCF_000185905.1:YP_004141620.1 142 RIAAMMPNMPETVAAMLAAASIGAVWSSCSPDFGEQGVLDRFGQIEPVVFIAPDGYWYNGKAIEVADKI 210
********************************************************************* PP
TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGv 278
++va +l+++++++++ y+g ++ +a ++ a+ le+ l+ + ++ fe lpf+hplyilfssGttG+
lcl|NCBI__GCF_000185905.1:YP_004141620.1 211 AAVAAKLGTVHKILVVDYLGTSSDVAGIIDKAVALEEALSPFAGKPVAFEPLPFSHPLYILFSSGTTGI 279
******************************************99************************* PP
TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347
pk+ivhsaGGtl+qh+keh+lh++ltdgdr++y+tt+Gwmmwn+lvsgla Gatl lydGsp+ p++nv
lcl|NCBI__GCF_000185905.1:YP_004141620.1 280 PKCIVHSAGGTLIQHVKEHRLHAGLTDGDRFFYFTTCGWMMWNWLVSGLASGATLLLYDGSPFYPDGNV 348
********************************************************************* PP
TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416
lfd+a++e++t lGtsak+++ vrk+glkp+rthdls++r++ stGspl+pe f++vy++ik dv+las
lcl|NCBI__GCF_000185905.1:YP_004141620.1 349 LFDFADAEKMTFLGTSAKFIDSVRKAGLKPIRTHDLSTVRAISSTGSPLSPEDFRFVYDGIKKDVHLAS 417
********************************************************************* PP
TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485
+sGGtdivscfv+++p+ pv+ Geiq+pglGlav++wd++G+pv++ekGelv++k++p+mp+ fwnd+d
lcl|NCBI__GCF_000185905.1:YP_004141620.1 418 VSGGTDIVSCFVLGVPTQPVWTGEIQGPGLGLAVDVWDDDGRPVRQEKGELVCAKAFPAMPIGFWNDPD 486
********************************************************************* PP
TIGR01217 486 GskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvig 554
G kyr+ayf+++++vw+hGd++e+t +Gg++ihGrsdatlnp+Gvr+G+aeiyn+ve+++e+ e+l+ig
lcl|NCBI__GCF_000185905.1:YP_004141620.1 487 GKKYRAAYFERFDNVWCHGDFAEWTEHGGLIIHGRSDATLNPGGVRIGTAEIYNQVEQMPEILEALCIG 555
********************************************************************* PP
TIGR01217 555 qeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdv 623
q+ ++ ++rv+lfv+la+G++lde+l k+i+ +ir+g+sprhvp++i++v++iprt+sGk+ e+av+dv
lcl|NCBI__GCF_000185905.1:YP_004141620.1 556 QDFDN-DVRVILFVRLAAGVQLDEDLEKRIRAKIRSGASPRHVPARIVAVTDIPRTKSGKITELAVRDV 623
*9977.*************************************************************** PP
TIGR01217 624 vaGkpvenkgalsnpealdlyeeleel 650
v+G++++nk+al+npeal+l+++l++l
lcl|NCBI__GCF_000185905.1:YP_004141620.1 624 VHGRAIKNKEALANPEALELFKNLPQL 650
************************987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (652 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: 00:00:00.04
# Mc/sec: 9.32
//
[ok]
This GapMind analysis is from Sep 24 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