Align acetoacetyl-CoA synthase (EC 2.3.1.194) (characterized)
to candidate WP_017219769.1 A923_RS0100990 acetoacetate--CoA ligase
Query= BRENDA::Q9JMI1
(672 letters)
>NCBI__GCF_000276805.1:WP_017219769.1
Length = 720
Score = 486 bits (1250), Expect = e-141
Identities = 281/726 (38%), Positives = 398/726 (54%), Gaps = 89/726 (12%)
Query: 18 MWEPDSKK--DTQMDRFRAAVGTACGLALGNYDDLYHWSVRSYSDFWAE---FWKFSGIV 72
+W P + ++ + R+ + L +Y L+ WS+ + + FW F+ F G
Sbjct: 9 IWTPSQARIDNSNITRYLQFLRLEYSLTFVHYQQLHQWSIDNTAVFWCSLVHFFNFKGNF 68
Query: 73 CSRMYDEVVDTSKGIADVPEWFRGSRLNYAENLL------------------------RH 108
+ V +WF S LN+AENLL +
Sbjct: 69 NLKR----VFVKNDCFYHCQWFPDSTLNFAENLLFPTVFSINKKSISINKNHVSTNCSHY 124
Query: 109 KEND-------RVALYVAREGREEIAKVTFEELRQQVALFAAAMRKMGVKKGDRVVGYLP 161
ND ++A+ RE + ++++++LR +V AAAMR++G+ KGDRV G LP
Sbjct: 125 SANDQDSVNPDKLAIICCREDGQR-TQLSYQQLRDEVTRVAAAMRELGIVKGDRVAGLLP 183
Query: 162 NSAHAVEAMLAAASIGAIWSSTSPDFGVNGVLDRFSQIQPKLIFSVEAVVYNGKEHGHLE 221
N + A+ AMLA SIGAIWSS SPDFG GVLDRF QI+P+L+F+ Y GK+ E
Sbjct: 184 NCSEAIIAMLATTSIGAIWSSCSPDFGHQGVLDRFIQIRPQLLFACNGYHYAGKQIDIRE 243
Query: 222 KLQRVVKGLPDLQRVVLIPYVLPREKIDISKIPNSMFLDDFLASG----TGAQAPQLEFE 277
K+ + LPDL ++V+IPY+ I LD A L FE
Sbjct: 244 KVNAIANVLPDLTQLVIIPYLALDVDIQTQANVTPSILDKTTVCHWRHFCAAIPRSLSFE 303
Query: 278 QLPFSHPLFIMFSSGTTGAPKCMVHSAGGTLIQHLKEHVLHGNMTSSDILLYYTTVGWMM 337
F+ PL+I++SSGTTG PKC+VHS GGTL+QH KE LH ++ D + YYTT GWMM
Sbjct: 304 ATAFADPLYILYSSGTTGMPKCIVHSVGGTLLQHAKELALHTDVQIDDRIFYYTTCGWMM 363
Query: 338 WNWMVSALATGASLVLYDGSPLVPTPNVLWDLVDRIGITILGTGAKWLSVLEEKDMKPME 397
WNW+VS+L+ GA+LVL+DGSP P VL++L D ++I G AK+ S ++ ++P E
Sbjct: 364 WNWLVSSLSQGATLVLFDGSPFYPHKQVLFELADTEKVSIFGASAKYYSACDKAKLRPAE 423
Query: 398 THNLHTLHTILSTGSPLKAQSYEYVYRCIKSTVLLGSISGGTDIISCFMGQNSSIPVYKG 457
T+ L L T+LSTGS L +S++Y+Y+ IK V L SI GGTDIISCFM ++PVY+G
Sbjct: 424 TYKLSNLKTMLSTGSTLSHESFDYIYQHIKQDVCLSSICGGTDIISCFMLGMPTLPVYRG 483
Query: 458 EIQARNLGMAVEAWDEEGKTVWGASGELVCTKPIPCQPTHFWNDENGSKYRKAYFSKYPG 517
E+Q LGM V G+LVC +P P PT FW D + KY AYFS++
Sbjct: 484 ELQCIGLGMDVAF----------MQGDLVCRQPFPSMPTGFWQDPDDRKYHDAYFSRFHN 533
Query: 518 VWAHGDYCR-----INP----------------------------KTGGIVMLGRSDGTL 544
+WAHGDY INP K G+++ GRSD L
Sbjct: 534 IWAHGDYGELIYHYINPNPELVKPIENKSESVADSGIKKSTDISIKQIGVIIHGRSDAVL 593
Query: 545 NPNGVRFGSSEIYNIVEAFDEVEDSLCVPQYNRDGEERVVLFLKMASGHTFQPDLVKHIR 604
NP GVR G++EIY VE +++S+ + Q RD + RV+LF+++++G L+ I+
Sbjct: 594 NPGGVRIGTAEIYRQVEKLPAIQESIAIGQQWRD-DVRVILFVRLSAGVELDSQLISQIK 652
Query: 605 DAIRLGLSARHVPSLILETQGIPYTINGKKVEVAVKQVIAGKTVEHRGAFSNPESLDLYR 664
IR + RHVP+ I+ IP TI+GK VE+AV+ V+ G +V ++ A +NPE+L L+
Sbjct: 653 QVIRTNTTPRHVPAKIIAVADIPKTISGKIVELAVRNVVHGISVTNKDALANPEALTLFA 712
Query: 665 DIPELQ 670
+ ELQ
Sbjct: 713 HLAELQ 718
Lambda K H
0.319 0.136 0.417
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: 1178
Number of extensions: 40
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 672
Length of database: 720
Length adjustment: 39
Effective length of query: 633
Effective length of database: 681
Effective search space: 431073
Effective search space used: 431073
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_017219769.1 A923_RS0100990 (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.283529.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.8e-238 778.8 8.2 4.6e-167 542.9 0.1 3.0 3 NCBI__GCF_000276805.1:WP_017219769.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017219769.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 55.1 0.2 2e-19 2e-19 4 96 .. 7 100 .. 4 125 .. 0.89
2 ! 542.9 0.1 4.6e-167 4.6e-167 102 509 .. 138 543 .. 107 547 .. 0.92
3 ! 184.7 0.5 1.2e-58 1.2e-58 513 651 .. 581 718 .. 573 719 .. 0.98
Alignments for each domain:
== domain 1 score: 55.1 bits; conditional E-value: 2e-19
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekev.vddsk 75
+++w+p + r+++++++r+ ++ ++ +++ +y++l++ws+d+ fw ++++f++ ++ + k+v v ++
NCBI__GCF_000276805.1:WP_017219769.1 7 DPIWTPSQARIDNSNITRYLQFLRLEYSLTFVHYQQLHQWSIDNTAVFWCSLVHFFNFKGNFNLKRVfVKNDC 79
589***********************************************************99998467777 PP
TIGR01217 76 mlaarffpgarlnyaenllrk 96
++fp+++ln+aenll
NCBI__GCF_000276805.1:WP_017219769.1 80 FYHCQWFPDSTLNFAENLLFP 100
88999*************965 PP
== domain 2 score: 542.9 bits; conditional E-value: 4.6e-167
TIGR01217 102 allyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfG 174
a++ e+ + +++++++lr v+++aaa+r+lG+ kGdrvag+lpn +ea+ a+lat+s+GaiwsscspdfG
NCBI__GCF_000276805.1:WP_017219769.1 138 AIICCREDGQRTQLSYQQLRDEVTRVAAAMRELGIVKGDRVAGLLPNCSEAIIAMLATTSIGAIWSSCSPDFG 210
556667778999************************************************************* PP
TIGR01217 175 argvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipyvg......dreklapkv.e. 239
+gvldrf qi+p+llf+++gy y Gk+ d rekv+++a+ lpdl + v+ipy+ ++++ p + +
NCBI__GCF_000276805.1:WP_017219769.1 211 HQGVLDRFIQIRPQLLFACNGYHYAGKQIDIREKVNAIANVLPDLTQLVIIPYLAldvdiqTQANVTPSIlDk 283
*****************************************************86222111223333333221 PP
TIGR01217 240 .galtledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrlly 311
++ + aa l fe f plyil+ssGttG+pk+ivhs GGtl+qh ke++lh+d++ dr++y
NCBI__GCF_000276805.1:WP_017219769.1 284 tTVCHWRHFCAA-IPRSLSFEATAFADPLYILYSSGTTGMPKCIVHSVGGTLLQHAKELALHTDVQIDDRIFY 355
123457778877.56789******************************************************* PP
TIGR01217 312 yttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdls 384
ytt+Gwmmwn+lvs+l Gatlvl+dGsp+ p+ +vlf+la+ e+++++G+saky sa+ k+ l+pa+t++ls
NCBI__GCF_000276805.1:WP_017219769.1 356 YTTCGWMMWNWLVSSLSQGATLVLFDGSPFYPHKQVLFELADTEKVSIFGASAKYYSACDKAKLRPAETYKLS 428
************************************************************************* PP
TIGR01217 385 alrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawdeeG 457
l++++stGs l+ e+f+y+y+ ik dv l+si GGtdi+scf+++ p+lpvy+Ge+q+ glG++v
NCBI__GCF_000276805.1:WP_017219769.1 429 NLKTMLSTGSTLSHESFDYIYQHIKQDVCLSSICGGTDIISCFMLGMPTLPVYRGELQCIGLGMDVAF----- 496
****************************************************************9965..... PP
TIGR01217 458 kpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyiel 509
+G+lv+ +p+psmp+ fw d+d ky++ayf+++ ++wahGdy el
NCBI__GCF_000276805.1:WP_017219769.1 497 -----MQGDLVCRQPFPSMPTGFWQDPDDRKYHDAYFSRFHNIWAHGDYGEL 543
.....579*****************************************876 PP
== domain 3 score: 184.7 bits; conditional E-value: 1.2e-58
TIGR01217 513 GgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585
g++ihGrsda lnp+Gvr+G+aeiy +ve+l+ ++es+ igq+++d ++rv+lfv+l++G++ld +l+ +ik
NCBI__GCF_000276805.1:WP_017219769.1 581 IGVIIHGRSDAVLNPGGVRIGTAEIYRQVEKLPAIQESIAIGQQWRD-DVRVILFVRLSAGVELDSQLISQIK 652
589********************************************.************************* PP
TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelk 651
+ ir++ +prhvp+kii+va+ip+t+sGk+ve+av++vv+G +v nk+al+npeal l+++l+el+
NCBI__GCF_000276805.1:WP_017219769.1 653 QVIRTNTTPRHVPAKIIAVADIPKTISGKIVELAVRNVVHGISVTNKDALANPEALTLFAHLAELQ 718
***************************************************************987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (720 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 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.55
//
[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