Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_013257294.1 DEBA_RS02325 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000143965.1:WP_013257294.1
Length = 650
Score = 721 bits (1862), Expect = 0.0
Identities = 361/646 (55%), Positives = 447/646 (69%), Gaps = 4/646 (0%)
Query: 6 PLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGE 65
PLW P E V R+ ++ FI + +R G A Y A H WS+ +R FW AVW+ C+V
Sbjct: 4 PLWTPSPERVARANLSRFIAFVNQRHGLDLAGYAALHAWSIDQRADFWRAVWDFCEVRAS 63
Query: 66 SGEKALVDG-DRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRAL 124
+A+ + M AR+F ARLNFAENLLR+ ALIF E RL+ +L A
Sbjct: 64 RPAEAVTQNPEAMPGARWFVGARLNFAENLLRQPDDRPALIFCNEIGHQRRLSRAQLLAA 123
Query: 125 VSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFG 184
RL +AL A G+G GDRVA MPN+PET+ MLATAS+GAIWSSCSPDFG QGV+DRFG
Sbjct: 124 SGRLSRALAAVGVGPGDRVAGFMPNIPETVIGMLATASLGAIWSSCSPDFGFQGVMDRFG 183
Query: 185 QIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVT 242
QI PK+ + DGY Y GKR D + V + + V+ PY D+ L+ + +
Sbjct: 184 QIRPKVMLCADGYPYGGKRFDCLERAALVGARIDSLERIVVAPYMTDAPDLSAAPKA-IA 242
Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
DF+AG GP F +LPF HPLYI++SSGTTG PKCIVH AGGTLLQHLKEH C L
Sbjct: 243 YDDFVAGHGDGPPAFAQLPFDHPLYIMYSSGTTGAPKCIVHGAGGTLLQHLKEHALQCDL 302
Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
+ LFYFTTCGWMMWNWL S LAVGA + LYDGSPF P VL+ + E +VFGTS
Sbjct: 303 TADDTLFYFTTCGWMMWNWLVSALAVGAAVALYDGSPFHPGPEVLWRMSQEEGVSVFGTS 362
Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
A+Y+ A+ K G PA DL L+ + STGSPL+PE F + Y+ IK D+ L+SISGGTDI
Sbjct: 363 ARYLAALEKSGLRPAEAFDLGRLKAVLSTGSPLAPEQFDWAYQNIKADMCLSSISGGTDI 422
Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
+SCF GNP+ PV+ G++Q PGLG+AV W++ G+ + G+KGELVC + FPSMPV FWND
Sbjct: 423 ISCFAGGNPIGPVYPGQLQAPGLGMAVQAWDENGRALWGQKGELVCVKPFPSMPVGFWND 482
Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542
PD KY++AYF RF VW HGD+ E TP GG++IHGRSDATLNPGGVRIGTAEIY QVE
Sbjct: 483 PDDEKYQSAYFRRFAGVWHHGDYCEMTPEGGVIIHGRSDATLNPGGVRIGTAEIYRQVEG 542
Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602
+ +VA++L +GQ W D RV+LFV++A G +L +A + I RIR +PRHVPAKI+AV
Sbjct: 543 LAQVADSLVVGQRWRGDERVILFVKMAPGHQLDQATAQAIATRIRQNTTPRHVPAKILAV 602
Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
DIP T SGK VE+AVR+V+ GRPV NK+ALANP+AL LFA EL
Sbjct: 603 DDIPYTISGKKVEMAVRNVIEGRPVTNKDALANPQALALFADRPEL 648
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: 1421
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: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space: 374544
Effective search space used: 374544
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_013257294.1 DEBA_RS02325 (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.24931.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
8.6e-285 931.9 0.0 9.6e-285 931.7 0.0 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013257294.1 DEBA_RS02325 acetoacetate--CoA l
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013257294.1 DEBA_RS02325 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 931.7 0.0 9.6e-285 9.6e-285 3 650 .. 2 648 .. 1 650 [] 0.99
Alignments for each domain:
== domain 1 score: 931.7 bits; conditional E-value: 9.6e-285
TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevv 71
+ +lw+p erv++a+l+rf+a+v +r+G+ l++y+al+ ws+d++ +fw+avw+f++v++s++ ++v
lcl|NCBI__GCF_000143965.1:WP_013257294.1 2 PTPLWTPSPERVARANLSRFIAFVNQRHGLDLAGYAALHAWSIDQRADFWRAVWDFCEVRASRPAEAVT 70
568****************************************************************99 PP
TIGR01217 72 dd.skmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkG 139
++ + m++ar+f garln+aenllr+ + +al++ +e + +++ ++l + +l+ al a+Gv++G
lcl|NCBI__GCF_000143965.1:WP_013257294.1 71 QNpEAMPGARWFVGARLNFAENLLRQPDDRPALIFCNEIGHQRRLSRAQLLAASGRLSRALAAVGVGPG 139
763789*************************************************************** PP
TIGR01217 140 drvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrek 208
drvag++pnipe+v +latas+GaiwsscspdfG +gv+drf+qi+pk++++ dgy y+Gk+ d e+
lcl|NCBI__GCF_000143965.1:WP_013257294.1 140 DRVAGFMPNIPETVIGMLATASLGAIWSSCSPDFGFQGVMDRFGQIRPKVMLCADGYPYGGKRFDCLER 208
********************************************************************* PP
TIGR01217 209 vrevakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttG 277
+ v + +l+++v+ py+ d+ l+ + a+ ++d++a+ ++++ f qlpfdhplyi++ssGttG
lcl|NCBI__GCF_000143965.1:WP_013257294.1 209 AALVGARIDSLERIVVAPYMTDAPDLSA-APKAIAYDDFVAGHGDGPPAFAQLPFDHPLYIMYSSGTTG 276
*********************9988877.89************************************** PP
TIGR01217 278 vpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatn 346
+pk+ivh aGGtl+qhlkeh+l cdlt d l+y+tt+Gwmmwn+lvs+la+Ga++ lydGsp+ p ++
lcl|NCBI__GCF_000143965.1:WP_013257294.1 277 APKCIVHGAGGTLLQHLKEHALQCDLTADDTLFYFTTCGWMMWNWLVSALAVGAAVALYDGSPFHPGPE 345
********************************************************************* PP
TIGR01217 347 vlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvlla 415
vl+++ + eg++v+Gtsa+y+ a++k+gl+pa+ +dl l++v+stGspl pe f++ y++ikad+ l+
lcl|NCBI__GCF_000143965.1:WP_013257294.1 346 VLWRMSQEEGVSVFGTSARYLAALEKSGLRPAEAFDLGRLKAVLSTGSPLAPEQFDWAYQNIKADMCLS 414
********************************************************************* PP
TIGR01217 416 sisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnde 484
sisGGtdi+scf+g+np pvy G++qapglG+av+awde+G++++g+kGelv+ kp+psmpv fwnd+
lcl|NCBI__GCF_000143965.1:WP_013257294.1 415 SISGGTDIISCFAGGNPIGPVYPGQLQAPGLGMAVQAWDENGRALWGQKGELVCVKPFPSMPVGFWNDP 483
********************************************************************* PP
TIGR01217 485 dGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvi 553
d ky++ayf ++ gvw hGdy+e+tp+Gg++ihGrsdatlnp+Gvr+G+aeiy +ve l +v++slv+
lcl|NCBI__GCF_000143965.1:WP_013257294.1 484 DDEKYQSAYFRRFAGVWHHGDYCEMTPEGGVIIHGRSDATLNPGGVRIGTAEIYRQVEGLAQVADSLVV 552
********************************************************************* PP
TIGR01217 554 gqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkd 622
gq ++ +erv+lfvk+a+G++ld+a + i +ir + +prhvp+ki++v++ip+t+sGkkve+av++
lcl|NCBI__GCF_000143965.1:WP_013257294.1 553 GQRWRG-DERVILFVKMAPGHQLDQATAQAIATRIRQNTTPRHVPAKILAVDDIPYTISGKKVEMAVRN 620
****95.************************************************************** PP
TIGR01217 623 vvaGkpvenkgalsnpealdlyeeleel 650
v++G+pv nk+al+np+al l+++ +el
lcl|NCBI__GCF_000143965.1:WP_013257294.1 621 VIEGRPVTNKDALANPQALALFADRPEL 648
***********************98876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (650 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 8.01
//
[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