Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011611958.1 TERY_RS11305 acetate--CoA ligase
Query= SwissProt::P31638
(660 letters)
>NCBI__GCF_000014265.1:WP_011611958.1
Length = 655
Score = 730 bits (1884), Expect = 0.0
Identities = 361/657 (54%), Positives = 472/657 (71%), Gaps = 13/657 (1%)
Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
IES++QE R+F PPE F A I +E Y+ L ++A+ + E FWA A L W + + K
Sbjct: 6 IESILQEKRLFQPPEKFVQTAQIKGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDK 65
Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
VL+ PF KWF +G++N SYNCLDR+L +K A+++E + G +TY +LH +V
Sbjct: 66 VLEWQ-PPFAKWFINGKINISYNCLDRHLTTWRRNKAALIWEGEPGDSRTITYAQLHREV 124
Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
C+ AN K LG++KGDRV IYMPM E +AM ACAR+GA H+VVFGGFSA +L+ RLVD
Sbjct: 125 CQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIGAPHTVVFGGFSADALKNRLVD 184
Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
A ++TAD R +PLK D AL + G +V NV+V +RT K+ GRD W
Sbjct: 185 AEAKLVVTADGGWRKDAIVPLKEQVDKAL-MAGAPSVENVLVVKRTAQKIQMEPGRDHWW 243
Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
D+ C AEP+ +E LF+LYTSG+TG PKGV H+TGGY L+ +T KW FD++
Sbjct: 244 HDLQKSASGECPAEPMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAFDLQD 303
Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P N G WD++ ++ V+IFYTA
Sbjct: 304 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCLWDVVEKYGVTIFYTA 363
Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
PTAIR+L+K E HP +L+SLRLLGTVGEPINPEAW+WY++ IG+ +CPIVDT+
Sbjct: 364 PTAIRALMKMGEQ----HPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKCPIVDTW 419
Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
WQTETGG MITPLPGATP PGS T P PGI+A IV+E G V NGG LVVK PWP M
Sbjct: 420 WQTETGGFMITPLPGATPTKPGSATFPFPGIIADIVNEEGESVDGNNGGYLVVKHPWPGM 479
Query: 484 IRTIWGDPERFRKSYFP---EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
+RT++GDP+RFR++Y+ + G +Y AGDG+ +D+D GYF +MGR+DDV+NV+GHR+
Sbjct: 480 MRTVYGDPDRFRRTYWEYLRPKNGEYIYFAGDGAHKDED-GYFWVMGRVDDVINVAGHRL 538
Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
GTME+ESALVS+P VAEAAVVG+PD++ GE I AFV L+ R E K EL+ V
Sbjct: 539 GTMEVESALVSHPAVAEAAVVGKPDEVKGEDIVAFVSLEGGREPDENLEK---ELKQHVV 595
Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657
KEIG IA+P +IRF D+LPKTRSGKIMRRLLRSLA G+EIT DTSTL++ ++L++L+
Sbjct: 596 KEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTSTLQDRSVLDKLR 652
Lambda K H
0.319 0.136 0.422
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: 1419
Number of extensions: 73
Number of successful extensions: 7
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: 660
Length of database: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space: 383774
Effective search space used: 383774
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 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate WP_011611958.1 TERY_RS11305 (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.29825.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1019.2 0.0 0 1019.0 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011611958.1 TERY_RS11305 acetate--CoA ligase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011611958.1 TERY_RS11305 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1019.0 0.0 0 0 2 627 .. 29 652 .. 28 654 .. 0.98
Alignments for each domain:
== domain 1 score: 1019.0 bits; conditional E-value: 0
TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek. 69
+ +e+ykelye+a+++pe+fwa+la++el+w+++++kvl+++ +p++kWf +g++n+sync+drh+++
lcl|NCBI__GCF_000014265.1:WP_011611958.1 29 KGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDKVLEWQ-PPFAKWFINGKINISYNCLDRHLTTw 96
6789*************************************9.89************************ PP
TIGR02188 70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
r++k+a+iweg+ +g dsr++tYa+l+revc++anv+k+lGvkkgdrv iY+pmipea+iamlacaRiG
lcl|NCBI__GCF_000014265.1:WP_011611958.1 97 RRNKAALIWEGE-PG-DSRTITYAQLHREVCQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIG 163
************.77.59*************************************************** PP
TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgee 207
a h+vvf+Gfsa+al++R+vdaeaklv+tad+g+R++ +++lk++vd+al + sve+vlvvkrt ++
lcl|NCBI__GCF_000014265.1:WP_011611958.1 164 APHTVVFGGFSADALKNRLVDAEAKLVVTADGGWRKDAIVPLKEQVDKALMAGAPSVENVLVVKRTAQK 232
***************************************************9999************** PP
TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
++ ++ grD+ww++l ++ as ec++e++dsed+lfiLYtsG+tG+PkGv+httgGy l++++t k+ f
lcl|NCBI__GCF_000014265.1:WP_011611958.1 233 IQ-MEPGRDHWWHDLQKS-ASGECPAEPMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAF 299
76.**************5.************************************************** PP
TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
d++d+d++wCtaDvGW+tGhsYivygPL+nGattl++eg+p+ ++++++w+v+eky+vtifYtaPtaiR
lcl|NCBI__GCF_000014265.1:WP_011611958.1 300 DLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCLWDVVEKYGVTIFYTAPTAIR 368
********************************************************************* PP
TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414
almk+ge+++++++l slr+lg+vGepinpeaw Wy++v+G++kcpivdtwWqtetGg++itplpg at
lcl|NCBI__GCF_000014265.1:WP_011611958.1 369 ALMKMGEQHPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKCPIVDTWWQTETGGFMITPLPG-AT 436
******************************************************************.6* PP
TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.... 479
++kpgsat P++Gi a++v+eeg++v+ +++ g+Lv+k+pwP+m+rt+ygd++rf +tY++ l+
lcl|NCBI__GCF_000014265.1:WP_011611958.1 437 PTKPGSATFPFPGIIADIVNEEGESVDGNNG-GYLVVKHPWPGMMRTVYGDPDRFRRTYWEYLRPknge 504
***************************9888.8***************************987666788 PP
TIGR02188 480 .lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivaf 547
+yf+GDga++d+dGy+w++GRvDdvinv+Ghrlgt+e+esalvsh+avaeaavvg+pde+kge ivaf
lcl|NCBI__GCF_000014265.1:WP_011611958.1 505 yIYFAGDGAHKDEDGYFWVMGRVDDVINVAGHRLGTMEVESALVSHPAVAEAAVVGKPDEVKGEDIVAF 573
89******************************************************************* PP
TIGR02188 548 vvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvst 616
v l+ g+e+de+ lekelk++v keig+ia+p +i+++++lPktRsGkimRRllr++a+g+e++gd+st
lcl|NCBI__GCF_000014265.1:WP_011611958.1 574 VSLEGGREPDEN-LEKELKQHVVKEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTST 641
***********5.******************************************************** PP
TIGR02188 617 ledpsvveelk 627
l+d+sv+++l+
lcl|NCBI__GCF_000014265.1:WP_011611958.1 642 LQDRSVLDKLR 652
********997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (655 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.07
//
[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