Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_012170770.1 AZC_RS11610 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000010525.1:WP_012170770.1
Length = 654
Score = 914 bits (2362), Expect = 0.0
Identities = 441/651 (67%), Positives = 513/651 (78%), Gaps = 2/651 (0%)
Query: 2 QAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCK 61
QA PLW P E + +S + I RFG S ++Y H WSV AFW VW+ C
Sbjct: 4 QAAHPLWQPGAERIAKSHVTWLIGEVNSRFGTSLSNYADLHAWSVKNLSAFWDLVWDSCG 63
Query: 62 VIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDEL 121
VIGE G + L+D D+M A+FFP+A+LNFAENLLRKTGSG+AL+FRGEDK+ RLT D+L
Sbjct: 64 VIGEKGAQRLIDADKMPGAQFFPDAKLNFAENLLRKTGSGEALVFRGEDKLEKRLTHDDL 123
Query: 122 RALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLD 181
ALVSRLQQAL+A+G+G GDRVAAMMPNMPETIA+MLA S+GAI+SSCSPDFGE+GVLD
Sbjct: 124 HALVSRLQQALKAEGVGVGDRVAAMMPNMPETIAIMLAATSLGAIFSSCSPDFGERGVLD 183
Query: 182 RFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAPT--VIVPYAGDSAALAPTVEG 239
RFGQI PK+F CDGYWYNGKR + K+ ++K L P+ V+VPY G++A A ++
Sbjct: 184 RFGQIEPKVFFACDGYWYNGKRVSIADKLVEISKHLTTPSKLVVVPYLGEAAETAGRLDR 243
Query: 240 GVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFH 299
GV L F+ F A + FERLPF HP+YILFSSGTTGVPKCIVH AGGTLLQHLKEHR+
Sbjct: 244 GVDLDAFLTPFAAKAVTFERLPFNHPIYILFSSGTTGVPKCIVHGAGGTLLQHLKEHRYQ 303
Query: 300 CGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVF 359
C L G++LFYFTTCGWMMWNWL SGLA TL L+DGSPF P VLFDYA E F VF
Sbjct: 304 CDLSPGDKLFYFTTCGWMMWNWLVSGLASELTLFLFDGSPFAPSPKVLFDYAQDEGFNVF 363
Query: 360 GTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGG 419
GTSAKYID++ K G P THDLS+LRL+TSTGSPL+PE F +VY GIK DV LASISGG
Sbjct: 364 GTSAKYIDSLHKEGLKPIETHDLSALRLITSTGSPLAPESFEYVYSGIKKDVHLASISGG 423
Query: 420 TDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMF 479
TDIVSCFVLG+P PVW+GEIQ GLG+AVDVW+++G+PV+ E+GELVCTR FPSMPVMF
Sbjct: 424 TDIVSCFVLGDPTAPVWKGEIQAAGLGMAVDVWSEDGRPVKLERGELVCTRPFPSMPVMF 483
Query: 480 WNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQ 539
WND DGAKY AAYFDRF N+WCHGDFA WT HGG+VI GRSDATLNP GVRIGTAEIY Q
Sbjct: 484 WNDKDGAKYHAAYFDRFPNIWCHGDFAMWTEHGGLVILGRSDATLNPQGVRIGTAEIYAQ 543
Query: 540 VEQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKI 599
VEQ+ +V E++ IGQDW++DVRVVLFVRL G L E L R IK +IR GASPRHVPAKI
Sbjct: 544 VEQIPDVMESVAIGQDWDNDVRVVLFVRLREGTTLDEDLVRRIKTQIRVGASPRHVPAKI 603
Query: 600 IAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
+ V DIPRT+SGKI ELAVR+VVHGRPVKN EAL+NPEALD + + +L S
Sbjct: 604 VQVTDIPRTRSGKITELAVREVVHGRPVKNTEALSNPEALDQYREVPDLLS 654
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: 1442
Number of extensions: 48
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: 654
Length adjustment: 38
Effective length of query: 612
Effective length of database: 616
Effective search space: 376992
Effective search space used: 376992
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_012170770.1 AZC_RS11610 (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.26615.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.6e-307 1007.0 0.0 1.9e-307 1006.8 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012170770.1 AZC_RS11610 acetoacetate--CoA li
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010525.1:WP_012170770.1 AZC_RS11610 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1006.8 0.0 1.9e-307 1.9e-307 4 650 .. 7 652 .. 3 654 .] 0.99
Alignments for each domain:
== domain 1 score: 1006.8 bits; conditional E-value: 1.9e-307
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72
++lw+p aer+++++++ ++ v rfG++l++y++l+ wsv++l+afw vw+ ++v+++++ ++++d
lcl|NCBI__GCF_000010525.1:WP_012170770.1 7 HPLWQPGAERIAKSHVTWLIGEVNSRFGTSLSNYADLHAWSVKNLSAFWDLVWDSCGVIGEKGAQRLID 75
68******************************************************************* PP
TIGR01217 73 dskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdr 141
+km++a+ffp+a+ln+aenllrk+gs++al++++e+k ++t+++l ++v++l++al+a Gv+ Gdr
lcl|NCBI__GCF_000010525.1:WP_012170770.1 76 ADKMPGAQFFPDAKLNFAENLLRKTGSGEALVFRGEDKLEKRLTHDDLHALVSRLQQALKAEGVGVGDR 144
********************************************************************* PP
TIGR01217 142 vagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvr 210
va+++pn+pe++a++la++s+Gai+sscspdfG+rgvldrf+qiepk++f++dgy+ynGk+ +k+
lcl|NCBI__GCF_000010525.1:WP_012170770.1 145 VAAMMPNMPETIAIMLAATSLGAIFSSCSPDFGERGVLDRFGQIEPKVFFACDGYWYNGKRVSIADKLV 213
********************************************************************* PP
TIGR01217 211 evakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvp 279
e+ k+l++ + v++py+g++++ a +++ +++l+ +l+ + a + fe+lpf+hp+yilfssGttGvp
lcl|NCBI__GCF_000010525.1:WP_012170770.1 214 EISKHLTTPSKLVVVPYLGEAAETAGRLDRGVDLDAFLTPFAAKAVTFERLPFNHPIYILFSSGTTGVP 282
********************************************************************* PP
TIGR01217 280 kaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvl 348
k+ivh aGGtl+qhlkeh++ cdl++gd+l+y+tt+Gwmmwn+lvsgla tl l+dGsp+ p+++vl
lcl|NCBI__GCF_000010525.1:WP_012170770.1 283 KCIVHGAGGTLLQHLKEHRYQCDLSPGDKLFYFTTCGWMMWNWLVSGLASELTLFLFDGSPFAPSPKVL 351
********************************************************************* PP
TIGR01217 349 fdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasi 417
fd+a+ eg+ v+Gtsaky++ ++k+glkp++thdlsalrl++stGspl pe+feyvy++ik dv+lasi
lcl|NCBI__GCF_000010525.1:WP_012170770.1 352 FDYAQDEGFNVFGTSAKYIDSLHKEGLKPIETHDLSALRLITSTGSPLAPESFEYVYSGIKKDVHLASI 420
********************************************************************* PP
TIGR01217 418 sGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedG 486
sGGtdivscfv++ p+ pv+kGeiqa glG+av++w e+G+pv+ e+Gelv+t+p+psmpv+fwnd+dG
lcl|NCBI__GCF_000010525.1:WP_012170770.1 421 SGGTDIVSCFVLGDPTAPVWKGEIQAAGLGMAVDVWSEDGRPVKLERGELVCTRPFPSMPVMFWNDKDG 489
********************************************************************* PP
TIGR01217 487 skyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigq 555
+ky++ayfd++p++w+hGd++ +t +Gg+vi+Grsdatlnp+Gvr+G+aeiy +ve++++v es+ igq
lcl|NCBI__GCF_000010525.1:WP_012170770.1 490 AKYHAAYFDRFPNIWCHGDFAMWTEHGGLVILGRSDATLNPQGVRIGTAEIYAQVEQIPDVMESVAIGQ 558
********************************************************************* PP
TIGR01217 556 eqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvv 624
++++ ++rvvlfv+l +G+tlde+lv++ik +ir+g+sprhvp+ki++v++iprt sGk+ e+av++vv
lcl|NCBI__GCF_000010525.1:WP_012170770.1 559 DWDN-DVRVVLFVRLREGTTLDEDLVRRIKTQIRVGASPRHVPAKIVQVTDIPRTRSGKITELAVREVV 626
**87.**************************************************************** PP
TIGR01217 625 aGkpvenkgalsnpealdlyeeleel 650
+G+pv+n +alsnpeald y+e+++l
lcl|NCBI__GCF_000010525.1:WP_012170770.1 627 HGRPVKNTEALSNPEALDQYREVPDL 652
**********************9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (654 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 9.39
//
[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