Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_029767366.1 HALAL_RS0104350 acetoacetate--CoA ligase
Query= BRENDA::D6EQU8
(658 letters)
>NCBI__GCF_000527155.1:WP_029767366.1
Length = 643
Score = 570 bits (1469), Expect = e-167
Identities = 291/641 (45%), Positives = 402/641 (62%), Gaps = 11/641 (1%)
Query: 9 LWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRFS 68
LW P + I F + + G Y L ++SVD+ TFW AV E+F +
Sbjct: 6 LWLPRPDAVDTTNIGEFGSRLSRQVGTDLTS-YPDLWQFSVDDPATFWGAVWEYFQLGEP 64
Query: 69 TPYARVLGDRTMPGAQWFPGATLNYAEHALRAAGTRPDEPALLYVDETHEPAPVTWAELR 128
P RVL + +MPGA WFP NYA+ L A G + A+ +T + T ELR
Sbjct: 65 VPSHRVLTEDSMPGAVWFPDQGFNYAKAVLNAPGMADTDVAIRAYSDTRDTFEWTLDELR 124
Query: 129 RQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSVLDR 188
VA L L A GV+ GDRV+ ++PNIP+ +LA A++G V+TSCAP+FGA++V+DR
Sbjct: 125 SMVARLRTGLLAHGVQKGDRVAAWMPNIPETHALMLAAASIGAVFTSCAPEFGAKAVIDR 184
Query: 189 FQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPT-LRAVIHIPLLGTEAPDGTLDWE 247
FQQV+P +LF DGY YG K +RR + ++ + LR+++ LG++ G WE
Sbjct: 185 FQQVKPTILFVTDGYMYGKKRIERRQEIEQVVETMEEDLRSIVTFNYLGSKTGVGK-SWE 243
Query: 248 TLTAADAEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGLHCDLGPGD 307
TAA+ E +E PF+HPL++LYSSGTTGLPKAIV GGI +EH K LGLH +LGPGD
Sbjct: 244 EFTAAEGELDFEMFPFEHPLYILYSSGTTGLPKAIVHGHGGIALEHAKMLGLHQNLGPGD 303
Query: 308 RFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERTGATLFGTSAAYV 367
RFFWY++TGWMMWN+L S L G +V +DG+P + WR+AE T FGTSA ++
Sbjct: 304 RFFWYSTTGWMMWNYLASAPLVGAALVTFDGAPD---PEGMWRMAEDAEVTYFGTSAPFL 360
Query: 368 MACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADLWIASVSGGTDVC 427
MACR G+ P DLS I + +TG+PLP GF ++++ + + S+SGGTD+C
Sbjct: 361 MACRDRGIVPKDVADLSRIHGIGSTGAPLPGVGFDYVYEAISDTAQ---LQSLSGGTDLC 417
Query: 428 SCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSMPIRFWNDP 487
+ F G P +PV GEL LG ++S+DP G + GELV+T PMPSMP+ W DP
Sbjct: 418 TGFVGGAPNVPVWRGELSCLCLGAKVESFDPDGHHALEREGELVITKPMPSMPVSLWGDP 477
Query: 488 DGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYEAVERL 547
RY D+Y +PG+W HGDWIT+T RGS +I GRSD+TLNR GVRMG+++ Y VE +
Sbjct: 478 LRDRYRDTYLTAFPGIWCHGDWITITDRGSAIISGRSDATLNRGGVRMGTSEFYTVVEGI 537
Query: 548 PEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPDEVIEV 607
+ +SLV+ ++ D + +FV G ++DD + RI IR LSPRHVPDE+ EV
Sbjct: 538 DGVVDSLVVHLDDDDDR--LIVFVQPTEGVSVDDDMRGRISTAIRAELSPRHVPDEIHEV 595
Query: 608 PGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLH 648
+P TL+GK+IEVP+K++L+G P+ +AV+ S+ N D ++
Sbjct: 596 GAVPRTLSGKKIEVPLKKILKGIPVSQAVSLESLANPDAMN 636
Lambda K H
0.320 0.138 0.442
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: 1463
Number of extensions: 77
Number of successful extensions: 5
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: 658
Length of database: 643
Length adjustment: 38
Effective length of query: 620
Effective length of database: 605
Effective search space: 375100
Effective search space used: 375100
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 (21.8 bits)
S2: 54 (25.4 bits)
Align candidate WP_029767366.1 HALAL_RS0104350 (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.9477.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
3.3e-220 718.5 0.0 4.4e-220 718.1 0.0 1.0 1 lcl|NCBI__GCF_000527155.1:WP_029767366.1 HALAL_RS0104350 acetoacetate--Co
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_029767366.1 HALAL_RS0104350 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 718.1 0.0 4.4e-220 4.4e-220 4 642 .. 4 636 .. 2 641 .. 0.96
Alignments for each domain:
== domain 1 score: 718.1 bits; conditional E-value: 4.4e-220
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72
+vlw p + v+ +++ +f + + ++G+ l+ y +l+++svd+ +fw avwe++++ + ++v+
lcl|NCBI__GCF_000527155.1:WP_029767366.1 4 EVLWLPRPDAVDTTNIGEFGSRLSRQVGTDLTSYPDLWQFSVDDPATFWGAVWEYFQLGEPVPSHRVLT 72
589*999999*********************************************************** PP
TIGR01217 73 dskmlaarffpgarlnyaenllrkkgs..edall.yvdeekesakvtfeelrrqvaslaaalralGvkk 138
++ m++a++fp+ +nya+ +l + g d+++ ++++++ + t +elr +va+l + l a Gv+k
lcl|NCBI__GCF_000527155.1:WP_029767366.1 73 EDSMPGAVWFPDQGFNYAKAVLNAPGMadTDVAIrAYSDTRDTFEWTLDELRSMVARLRTGLLAHGVQK 141
***********************98875444454144566999************************** PP
TIGR01217 139 GdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrre 207
Gdrva+++pnipe+ a++la+as+Ga+++sc+p+fGa++v+drf+q++p +lf+ dgy+y+ k+ +rr+
lcl|NCBI__GCF_000527155.1:WP_029767366.1 142 GDRVAAWMPNIPETHALMLAAASIGAVFTSCAPEFGAKAVIDRFQQVKPTILFVTDGYMYGKKRIERRQ 210
********************************************************************* PP
TIGR01217 208 kvrevakelp.dlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGt 275
++++v+ + dlr++v y+g++ + + +e+++aa ++el fe pf+hplyil+ssGt
lcl|NCBI__GCF_000527155.1:WP_029767366.1 211 EIEQVVETMEeDLRSIVTFNYLGSKTGV------GKSWEEFTAA--EGELDFEMFPFEHPLYILYSSGT 271
*****9998538***********44433......569*******..*********************** PP
TIGR01217 276 tGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpa 344
tG+pkaivh GG+ ++h k ++lh +l++gdr+++y+t+Gwmmwn+l+s+ ++Ga+lv +dG+ p+
lcl|NCBI__GCF_000527155.1:WP_029767366.1 272 TGLPKAIVHGHGGIALEHAKMLGLHQNLGPGDRFFWYSTTGWMMWNYLASAPLVGAALVTFDGA---PD 337
***************************************************************7...69 PP
TIGR01217 345 tnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvl 413
++ ++++ae +t +Gtsa +++a+r++g+ p dls ++ + stG+pl+ gf+yvye+i + +
lcl|NCBI__GCF_000527155.1:WP_029767366.1 338 PEGMWRMAEDAEVTYFGTSAPFLMACRDRGIVPKDVADLSRIHGIGSTGAPLPGVGFDYVYEAISDTAQ 406
99******************************************************************* PP
TIGR01217 414 lasisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwn 482
l s+sGGtd+++ fvg+ p +pv++Ge+ + lG +ve++d++G+ + +Gelv+tkp+psmpv +w
lcl|NCBI__GCF_000527155.1:WP_029767366.1 407 LQSLSGGTDLCTGFVGGAPNVPVWRGELSCLCLGAKVESFDPDGHHALEREGELVITKPMPSMPVSLWG 475
********************************************************************* PP
TIGR01217 483 dedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveesl 551
d+ +yr++y+ +pg+w+hGd+i++t rG+ +i Grsdatln++Gvr+G++e y +ve +d v +sl
lcl|NCBI__GCF_000527155.1:WP_029767366.1 476 DPLRDRYRDTYLTAFPGIWCHGDWITITDRGSAIISGRSDATLNRGGVRMGTSEFYTVVEGIDGVVDSL 544
********************************************************************* PP
TIGR01217 552 vigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevav 620
v+ + +d r+++fv+ ++G+ +d+++ +i aira+lsprhvp++i ev +prtlsGkk+ev++
lcl|NCBI__GCF_000527155.1:WP_029767366.1 545 VVHLDDDD--DRLIVFVQPTEGVSVDDDMRGRISTAIRAELSPRHVPDEIHEVGAVPRTLSGKKIEVPL 611
**998777..89********************************************************* PP
TIGR01217 621 kdvvaGkpve...nkgalsnpeald 642
k++++G pv ++l+np+a++
lcl|NCBI__GCF_000527155.1:WP_029767366.1 612 KKILKGIPVSqavSLESLANPDAMN 636
*********9666678999999986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (643 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: 11.55
//
[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