Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_041098277.1 SUTH_RS07420 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000828635.1:WP_041098277.1
Length = 659
Score = 766 bits (1979), Expect = 0.0
Identities = 387/653 (59%), Positives = 471/653 (72%), Gaps = 10/653 (1%)
Query: 6 PLWVPDREIVERSPMAEFIDWCGERFGRSFA--DYDAFHDWSVSERGAFWTAVWEHCKVI 63
P+W P + + + + F +R+ R A DY H WS+ FW +VWE +V
Sbjct: 7 PIWQPSAQCIAGTRLTAFTKAAAKRWNRRLASADYLTLHAWSIDHPEEFWASVWEFGEVR 66
Query: 64 GESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRA 123
GE G +V+ ++M A++FP+ARLNFAENLLR+ GDAL+F GED+V R + +L
Sbjct: 67 GEMGSTIVVNREKMPGAKWFPQARLNFAENLLRRRDDGDALVFWGEDRVRGRASHADLYR 126
Query: 124 LVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRF 183
V++ ALRA G+ GDRVAA +PN+P + MLATAS+GAI+SS SPDFG QGV+DRF
Sbjct: 127 AVAQTAAALRAMGVVKGDRVAAYLPNLPAAVVAMLATASIGAIFSSASPDFGVQGVVDRF 186
Query: 184 GQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGV 241
GQI PK+ CDGY+YNGK D KV +A + + V+VPYAG ++ V+ GV
Sbjct: 187 GQIEPKVLFACDGYFYNGKTIDCLGKVADIAARMPSLERVVVVPYAGGGGDIS-AVKHGV 245
Query: 242 TLADFIAGFQAG-PLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300
LADF+A F + FERLPF HPLYI++SSGTTGVPKCIVH AGG LLQH+KEH+
Sbjct: 246 ALADFLAPFAGERDIRFERLPFDHPLYIMYSSGTTGVPKCIVHCAGGVLLQHIKEHQLQS 305
Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360
+R +RLFYFTTCGWMMWNWL S LA GATL LYDGSPF GN+LFDYA AE G
Sbjct: 306 DVRANDRLFYFTTCGWMMWNWLVSALASGATLLLYDGSPFVGRGNILFDYADAEGMTHLG 365
Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420
TSAK+IDA+ K P +TH L +R + STGSPL EGF +VY IK +VQLAS+SGGT
Sbjct: 366 TSAKFIDAIAKIELKPCQTHKLEHVRAVFSTGSPLVAEGFDYVYANIKQNVQLASVSGGT 425
Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480
DI+SCFV+GNP PV+RGEIQ GLG+AV V++D G+PVRGEKGELVCTR+FP MP+ FW
Sbjct: 426 DIISCFVIGNPNGPVYRGEIQCAGLGMAVGVFDDAGRPVRGEKGELVCTRSFPVMPIGFW 485
Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540
D GAKY AAYF+RFDN+WCHGDFAE T HGG +I+GRSDATLNPGGVRIGTAEIY QV
Sbjct: 486 KDEGGAKYHAAYFERFDNIWCHGDFAEITAHGGFIIYGRSDATLNPGGVRIGTAEIYRQV 545
Query: 541 EQMDEVAEALCIGQDW----EDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVP 596
E++ EV E++ IGQDW DVRVVLFV+L + L +AL + IK I+ +PRHVP
Sbjct: 546 EKLPEVVESIVIGQDWPPGNSGDVRVVLFVKLREALVLDDALEKRIKQVIKDNTTPRHVP 605
Query: 597 AKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
AKI+ VADIPRTKSGKIVELAVR+VVHG VKN EALANPEAL+ F EL+
Sbjct: 606 AKILQVADIPRTKSGKIVELAVRNVVHGAAVKNVEALANPEALEHFRDRAELQ 658
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: 1398
Number of extensions: 59
Number of successful extensions: 4
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: 659
Length adjustment: 38
Effective length of query: 612
Effective length of database: 621
Effective search space: 380052
Effective search space used: 380052
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 WP_041098277.1 SUTH_RS07420 (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.23177.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
6e-286 935.7 0.0 7e-286 935.5 0.0 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041098277.1 SUTH_RS07420 acetoacetate--CoA l
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041098277.1 SUTH_RS07420 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 935.5 0.0 7e-286 7e-286 5 651 .. 7 658 .. 3 659 .] 0.98
Alignments for each domain:
== domain 1 score: 935.5 bits; conditional E-value: 7e-286
TIGR01217 5 vlwepdaervkdarlarfraavgerfGa..algdydalyrwsvdeldafwkavwefsdvvfssaekevv 71
++w+p a+ ++ +rl+ f +a+++r+ + a +dy l+ ws+d+ ++fw++vwef +v+++ + vv
lcl|NCBI__GCF_000828635.1:WP_041098277.1 7 PIWQPSAQCIAGTRLTAFTKAAAKRWNRrlASADYLTLHAWSIDHPEEFWASVWEFGEVRGEMGSTIVV 75
79***********************9987899************************************* PP
TIGR01217 72 ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
+ +km++a++fp+arln+aenllr+++ +dal++ +e+++ + ++++l r va+ aaalra+Gv kGd
lcl|NCBI__GCF_000828635.1:WP_041098277.1 76 NREKMPGAKWFPQARLNFAENLLRRRDDGDALVFWGEDRVRGRASHADLYRAVAQTAAALRAMGVVKGD 144
********************************************************************* PP
TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
rva+ylpn+p av+a+latas+Gai+ss+spdfG++gv+drf+qiepk+lf++dgy ynGk d kv
lcl|NCBI__GCF_000828635.1:WP_041098277.1 145 RVAAYLPNLPAAVVAMLATASIGAIFSSASPDFGVQGVVDRFGQIEPKVLFACDGYFYNGKTIDCLGKV 213
********************************************************************* PP
TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaa.aqaaelvfeqlpfdhplyilfssGttG 277
+++a +p+l++vv++py+g ++ v+ ++ l+d+la a + ++ fe+lpfdhplyi++ssGttG
lcl|NCBI__GCF_000828635.1:WP_041098277.1 214 ADIAARMPSLERVVVVPYAGGGGDISA-VKHGVALADFLAPfAGERDIRFERLPFDHPLYIMYSSGTTG 281
********************8888877.9***********95567889********************* PP
TIGR01217 278 vpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatn 346
vpk+ivh aGG+l+qh+keh+l +d++ drl+y+tt+Gwmmwn+lvs+la Gatl lydGsp+v +n
lcl|NCBI__GCF_000828635.1:WP_041098277.1 282 VPKCIVHCAGGVLLQHIKEHQLQSDVRANDRLFYFTTCGWMMWNWLVSALASGATLLLYDGSPFVGRGN 350
********************************************************************* PP
TIGR01217 347 vlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvlla 415
+lfd+a++eg+t lGtsak+++a+ k +lkp +th+l+ +r+v stGspl +egf+yvy +ik +v+la
lcl|NCBI__GCF_000828635.1:WP_041098277.1 351 ILFDYADAEGMTHLGTSAKFIDAIAKIELKPCQTHKLEHVRAVFSTGSPLVAEGFDYVYANIKQNVQLA 419
********************************************************************* PP
TIGR01217 416 sisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnde 484
s+sGGtdi+scfv +np pvy+Geiq+ glG+av ++d+ G+pv+gekGelv+t+++p mp+ fw de
lcl|NCBI__GCF_000828635.1:WP_041098277.1 420 SVSGGTDIISCFVIGNPNGPVYRGEIQCAGLGMAVGVFDDAGRPVRGEKGELVCTRSFPVMPIGFWKDE 488
********************************************************************* PP
TIGR01217 485 dGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvi 553
G+ky++ayf++++++w+hGd++e+t++Gg +i+Grsdatlnp+Gvr+G+aeiy +ve+l+ev es+vi
lcl|NCBI__GCF_000828635.1:WP_041098277.1 489 GGAKYHAAYFERFDNIWCHGDFAEITAHGGFIIYGRSDATLNPGGVRIGTAEIYRQVEKLPEVVESIVI 557
********************************************************************* PP
TIGR01217 554 gqeqe...dgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkveva 619
gq+++ g++rvvlfvkl + ld+al k+ik+ i+ + +prhvp+ki++va+iprt+sGk+ve+a
lcl|NCBI__GCF_000828635.1:WP_041098277.1 558 GQDWPpgnSGDVRVVLFVKLREALVLDDALEKRIKQVIKDNTTPRHVPAKILQVADIPRTKSGKIVELA 626
****73335799********************************************************* PP
TIGR01217 620 vkdvvaGkpvenkgalsnpealdlyeeleelk 651
v++vv+G +v+n +al+npeal+ +++ +el+
lcl|NCBI__GCF_000828635.1:WP_041098277.1 627 VRNVVHGAAVKNVEALANPEALEHFRDRAELQ 658
***************************99987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (659 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: 10.29
//
[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