Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_101587717.1 BJEO58_RS03345 acetate--CoA ligase
Query= SwissProt::P9WQD1
(651 letters)
>NCBI__GCF_900169175.1:WP_101587717.1
Length = 697
Score = 676 bits (1743), Expect = 0.0
Identities = 347/671 (51%), Positives = 444/671 (66%), Gaps = 54/671 (8%)
Query: 22 ANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWS----------GAPF-----AK 66
A A+ E +R+AFW +QA+RL W P+ + GAP +
Sbjct: 14 AEPTAQTEPRTEAERVAFWERQASRLDWAKPWHTAHAFERPQRIGTREDGAPDFTVPRIE 73
Query: 67 WFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDL 126
WF GG LN A+NC+DRHVEAG GD+ A+ +EGEP GDRRTLTY+DL EVS+AANAL L
Sbjct: 74 WFAGGTLNAAHNCLDRHVEAGFGDKPALLFEGEP-GDRRTLTYADLQEEVSRAANALVSL 132
Query: 127 GLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITAD 186
G+ AGDRV IYLP+IPE VI LACAR+G +HS+VFGGF+A ALQ R+ D AK+L+T+D
Sbjct: 133 GVEAGDRVVIYLPVIPETVIVTLACARIGAVHSLVFGGFSADALQFRVEDTGAKVLVTSD 192
Query: 187 GQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVGSASPA 246
GQFRRG+ P+K AAD+A++ D +EHVLV+RRTG ++AW++GRD WWH + +ASP
Sbjct: 193 GQFRRGRAVPVKDAADQAVSG--DNDIEHVLVIRRTGDDIAWTDGRDAWWHEALAAASPD 250
Query: 247 HTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDV------------ 294
H P+ FD+EHPLF++YTSGTTG+PKG++HT+GGYLTQ YT +FD+
Sbjct: 251 HEPQQFDAEHPLFIIYTSGTTGRPKGLVHTTGGYLTQTAYTHALLFDLVDGELDAANDPQ 310
Query: 295 KPDSDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIY 354
K V WCTAD+ WVT HTY +YGPL NGVT+V+YEGTP P RHF+IIE+YGVT Y
Sbjct: 311 KVADAVHWCTADLAWVTAHTYEIYGPLLNGVTQVIYEGTPQVPHAGRHFEIIERYGVTTY 370
Query: 355 YTAPTLIRMFM-------KWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRT 407
YTAPTL+R M G D DLSS+RL+G+VGE +NPEAW W R +G G
Sbjct: 371 YTAPTLVRSHMGAFGSRPAAGERPADRWDLSSVRLVGTVGESVNPEAWSWLRREVGAGTA 430
Query: 408 PLVDTWWQTETGSAMISPLPGIA---------AAKPGSAMTPLPGISAKIVDDHGDPLPP 458
P++DTWWQ+ETGS ++SP P A A KPG A LPG+SA +VD G P P
Sbjct: 431 PVIDTWWQSETGSCVMSPRPHDACWDAETTPDAPKPGCATRALPGLSAAVVDADGSPAPT 490
Query: 459 HTEGAQHVTGYLVLDQPWPSMLRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAI 518
+ G LV+D PS R +W +P R+ SYW+ F ++G++ +GDGAR D +G I
Sbjct: 491 DEQ------GLLVVDGIGPSAARTVWNEPQRFLDSYWAHFGERGWFLSGDGARRDAEGDI 544
Query: 519 WVLGRIDDVMNVSGHRISTAEVESALVAHSGVAEAAVVGVTDETTTQAICAFVVL--RAN 576
VLGR+DDV+N+SGHR+ST E+ESALV+H V EA TD T A+ +FVVL A
Sbjct: 545 TVLGRVDDVINISGHRLSTIEIESALVSHPWVVEAGAAPTTDPLTGHAVLSFVVLSQEAP 604
Query: 577 YAPHDRTAEELRTEVARVISPIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTS 636
D + LR V+ I PIA+P + VPE+PKTRSGKIMRRLL + E+ LGDT+
Sbjct: 605 GVSGDDLRDTLRAHVSHRIGPIAKPAHIIAVPEVPKTRSGKIMRRLLTQLFEHTTLGDTT 664
Query: 637 TLLDPTVFDAI 647
+L + D I
Sbjct: 665 SLTNAHAVDDI 675
Lambda K H
0.319 0.136 0.433
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: 1587
Number of extensions: 96
Number of successful extensions: 9
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: 651
Length of database: 697
Length adjustment: 39
Effective length of query: 612
Effective length of database: 658
Effective search space: 402696
Effective search space used: 402696
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_101587717.1 BJEO58_RS03345 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# 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/TIGR02188.hmm
# target sequence database: /tmp/gapView.100953.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02188 [M=629]
Accession: TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.2e-227 742.2 0.0 3.5e-227 741.5 0.0 1.3 1 NCBI__GCF_900169175.1:WP_101587717.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900169175.1:WP_101587717.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 741.5 0.0 3.5e-227 3.5e-227 9 627 .. 19 676 .. 11 678 .. 0.90
Alignments for each domain:
== domain 1 score: 741.5 bits; conditional E-value: 3.5e-227
TIGR02188 9 elyeeaiedpekfwaklakeelewlkpfekvldeslep...............kvkWfedgelnvsyncvdrh 66
++ ++++++ +fw+++a++ l+w+kp+++ + ++ +++Wf++g+ln++ nc+drh
NCBI__GCF_900169175.1:WP_101587717.1 19 QTEPRTEAERVAFWERQASR-LDWAKPWHTAHAFERPQrigtredgapdftvpRIEWFAGGTLNAAHNCLDRH 90
55566788899********5.*******998654432211111112223444579****************** PP
TIGR02188 67 vek.rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
ve+ dk a+ +eg+ +g d+r+ltYa+l++ev+r+an+l +lGv+ gdrv+iYlp+ipe+vi+ lacaRiG
NCBI__GCF_900169175.1:WP_101587717.1 91 VEAgFGDKPALLFEGE-PG-DRRTLTYADLQEEVSRAANALVSLGVEAGDRVVIYLPVIPETVIVTLACARIG 161
***99***********.77.59*************************************************** PP
TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaew 211
avhs+vf+Gfsa+al+ R++d+ ak+++t+d+++R+g+++++k+++d+a++ + ++e+vlv++rtg+++a w
NCBI__GCF_900169175.1:WP_101587717.1 162 AVHSLVFGGFSADALQFRVEDTGAKVLVTSDGQFRRGRAVPVKDAADQAVSGDN-DIEHVLVIRRTGDDIA-W 232
***************************************************887.7*************77.* PP
TIGR02188 212 kegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikded.. 282
++grD ww+e+++ as ++ep+++d+e+plfi+YtsG+tG+PkG++httgGyl+++a+t+ ++fd+ d++
NCBI__GCF_900169175.1:WP_101587717.1 233 TDGRDAWWHEALAA-ASPDHEPQQFDAEHPLFIIYTSGTTGRPKGLVHTTGGYLTQTAYTHALLFDLVDGEld 304
*************5.***************************************************9764322 PP
TIGR02188 283 ...........ifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344
++wCtaD+ Wvt h+Y +ygPL+nG+t++++eg+p++p+a+r++e+ie+y+vt++YtaPt++
NCBI__GCF_900169175.1:WP_101587717.1 305 aandpqkvadaVHWCTADLAWVTAHTYEIYGPLLNGVTQVIYEGTPQVPHAGRHFEIIERYGVTTYYTAPTLV 377
2222333333479************************************************************ PP
TIGR02188 345 Ralm.......klgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplp 410
R+ m ++ge ++ dlss+r++g+vGe +npeaw+W++++vG + +p++dtwWq etG+ +++p p
NCBI__GCF_900169175.1:WP_101587717.1 378 RSHMgafgsrpAAGERPADRWDLSSVRLVGTVGESVNPEAWSWLRREVGAGTAPVIDTWWQSETGSCVMSPRP 450
*998433333335789999*****************************************************9 PP
TIGR02188 411 gv......atel....kpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetY 473
+ + kpg+at+ l+G++a+vvd +g+++ ++e+ g+Lv++ Ps +rt++++++rf ++Y
NCBI__GCF_900169175.1:WP_101587717.1 451 HDacwdaeT--TpdapKPGCATRALPGLSAAVVDADGSPAPTDEQ-GLLVVDGIGPSAARTVWNEPQRFLDSY 520
753232222..133449************************9999.8************************** PP
TIGR02188 474 fkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544
+ ++ + +++GDgarrd++G+i++lGRvDdvin+sGhrl+t+eiesalvsh+ v ea + ++d ++g+a+
NCBI__GCF_900169175.1:WP_101587717.1 521 WAHFGErgWFLSGDGARRDAEGDITVLGRVDDVINISGHRLSTIEIESALVSHPWVVEAGAAPTTDPLTGHAV 593
***977679**************************************************************** PP
TIGR02188 545 vafvvlkegve.edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvst 616
++fvvl++++ + ++l+++l+++v+++igpiakp++i v+e+PktRsGkimRRll ++ e +++lgd++
NCBI__GCF_900169175.1:WP_101587717.1 594 LSFVVLSQEAPgVSGDDLRDTLRAHVSHRIGPIAKPAHIIAVPEVPKTRSGKIMRRLLTQLFE-HTTLGDTTS 665
******99987345568********************************************98.56788**** PP
TIGR02188 617 ledpsvveelk 627
l + ++v+++
NCBI__GCF_900169175.1:WP_101587717.1 666 LTNAHAVDDIA 676
*******9986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (697 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: 12.98
//
[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