Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011386526.1 AMB_RS21140 acetate--CoA ligase
Query= SwissProt::P27550
(652 letters)
>NCBI__GCF_000009985.1:WP_011386526.1
Length = 645
Score = 937 bits (2422), Expect = 0.0
Identities = 439/646 (67%), Positives = 538/646 (83%), Gaps = 6/646 (0%)
Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60
MS+++ +PA A LI+ +Y Y++S+ PD FWGE GK +DWIKP+ KVKN S+
Sbjct: 1 MSEVYP--VPAETAKNALIDNDKYNEWYERSVKDPDGFWGEHGKRIDWIKPFTKVKNVSY 58
Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120
+ G+VSIKW+EDGTLN++ANCLDRHL + D+TAIIWEGDD ++S HI+Y +LH VCR
Sbjct: 59 S-GDVSIKWFEDGTLNVSANCLDRHLAKRRDQTAIIWEGDDPNESAHITYGDLHERVCRL 117
Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180
AN + +LG+KKGD V IY+PM+PEAAVAMLACAR+GAVHS++FGGFSP+A+AGRI D +S
Sbjct: 118 ANAMTDLGVKKGDRVTIYLPMIPEAAVAMLACARVGAVHSIVFGGFSPDALAGRIQDCDS 177
Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240
L+IT+DEG+R GR +PLK NVD AL+ S + V+V+KRTGG I GRD W+HDL
Sbjct: 178 SLLITADEGLRGGRKVPLKANVDKALET--CWSCKSVIVVKRTGGDIHMVTGRDHWYHDL 235
Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300
V +A+ H EM+AEDPLF+LYTSGSTGKPKGV+HTTGGYLVYA++T +YVFDYH GDI
Sbjct: 236 VAKAAPTHTPVEMSAEDPLFLLYTSGSTGKPKGVVHTTGGYLVYASMTHQYVFDYHEGDI 295
Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360
YWCTADVGWVTGHSY++YGPLA GA TLMFEG+PN+PT +R VVDKH+VNI YTAPTA
Sbjct: 296 YWCTADVGWVTGHSYIVYGPLANGAITLMFEGIPNYPTVSRFWDVVDKHKVNIFYTAPTA 355
Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420
IR+LM EG++ ++ T R+SLR+LGSVGEPINPEAW WY + +G+ +CP+VDTWWQTETGG
Sbjct: 356 IRSLMREGEEPVKKTSRASLRLLGSVGEPINPEAWTWYHRVVGDGRCPIVDTWWQTETGG 415
Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITD-SWPGQARTLFG 479
+ITPLPGAT LK GSATRPFFGV+P +VD EG LEGA EG+L + + WPGQ RTL+G
Sbjct: 416 ILITPLPGATALKPGSATRPFFGVKPVMVDAEGKTLEGAVEGNLCLAEPGWPGQMRTLWG 475
Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539
DHERF+Q+YF+T++ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH
Sbjct: 476 DHERFKQSYFATYQGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVAH 535
Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599
PK+AEAAVVG PH+IKGQ IYAYVTL GEEPS +L E+ NWVRKEIGP+A+PD++ W+
Sbjct: 536 PKVAEAAVVGYPHDIKGQGIYAYVTLVAGEEPSEDLRKELVNWVRKEIGPIASPDLIQWS 595
Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
LPKTRSGKIMRRILRKIA D +LGDTSTLADPGVV+ L++ +
Sbjct: 596 PGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPGVVDDLIDSR 641
Lambda K H
0.317 0.135 0.421
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: 1505
Number of extensions: 59
Number of successful extensions: 4
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: 652
Length of database: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space: 372698
Effective search space used: 372698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)
Align candidate WP_011386526.1 AMB_RS21140 (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.7926.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 1034.0 0.0 0 1033.8 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386526.1 AMB_RS21140 acetate--CoA ligase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386526.1 AMB_RS21140 acetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1033.8 0.0 0 0 3 628 .. 18 639 .. 16 640 .. 0.98
Alignments for each domain:
== domain 1 score: 1033.8 bits; conditional E-value: 0
TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvek 69
++++y+e+ye++++dp+ fw++++k +++w+kpf+kv++ s + ++kWfedg+lnvs+nc+drh++k
lcl|NCBI__GCF_000009985.1:WP_011386526.1 18 DNDKYNEWYERSVKDPDGFWGEHGK-RIDWIKPFTKVKNVSYSGdvSIKWFEDGTLNVSANCLDRHLAK 85
6799*********************.5************99887679********************** PP
TIGR02188 70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138
r+d++aiiwegd+++e s ++tY +l+++vcrlan++++lGvkkgdrv+iYlpmipea++amlacaR+G
lcl|NCBI__GCF_000009985.1:WP_011386526.1 86 RRDQTAIIWEGDDPNE-SAHITYGDLHERVCRLANAMTDLGVKKGDRVTIYLPMIPEAAVAMLACARVG 153
**************96.**************************************************** PP
TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgee 207
avhs+vf+Gfs++ala Ri+d+++ l+itadeglRgg++++lk++vd+ale++ s ++v+vvkrtg +
lcl|NCBI__GCF_000009985.1:WP_011386526.1 154 AVHSIVFGGFSPDALAGRIQDCDSSLLITADEGLRGGRKVPLKANVDKALETCW-SCKSVIVVKRTGGD 221
*****************************************************8.8************* PP
TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
++ ++ grD+w+++lv+k a +++p ++++edplf+LYtsGstGkPkGv+httgGyl++a++t++yvf
lcl|NCBI__GCF_000009985.1:WP_011386526.1 222 IH-MVTGRDHWYHDLVAK-AAPTHTPVEMSAEDPLFLLYTSGSTGKPKGVVHTTGGYLVYASMTHQYVF 288
77.**************7.99999********************************************* PP
TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
d++++di+wCtaDvGWvtGhsYivygPLanGa tl+feg+p+yp+ srfw+v++k+kv+ifYtaPtaiR
lcl|NCBI__GCF_000009985.1:WP_011386526.1 289 DYHEGDIYWCTADVGWVTGHSYIVYGPLANGAITLMFEGIPNYPTVSRFWDVVDKHKVNIFYTAPTAIR 357
********************************************************************* PP
TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414
+lm++gee vkk+++ slr+lgsvGepinpeaw+Wy++vvG+++cpivdtwWqtetGgilitplpg at
lcl|NCBI__GCF_000009985.1:WP_011386526.1 358 SLMREGEEPVKKTSRASLRLLGSVGEPINPEAWTWYHRVVGDGRCPIVDTWWQTETGGILITPLPG-AT 425
******************************************************************.6* PP
TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkp.wPsmlrtiygdeerfvetYfkklkglyf 482
+lkpgsat+P+fG+++++vd egk++e e g L++ +p wP+++rt++gd+erf ++Yf +++g+yf
lcl|NCBI__GCF_000009985.1:WP_011386526.1 426 ALKPGSATRPFFGVKPVMVDAEGKTLEGAVE-GNLCLAEPgWPGQMRTLWGDHERFKQSYFATYQGMYF 493
***************************8888.79***9988**************************** PP
TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
tGDgarrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h++vaeaavvg+p++ikg+ i+a+v+l
lcl|NCBI__GCF_000009985.1:WP_011386526.1 494 TGDGARRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVVGYPHDIKGQGIYAYVTLV 562
********************************************************************* PP
TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstled 619
+g+e++e+ l+kel ++vrkeigpia+pd i++ + lPktRsGkimRR+lrkiae++ +lgd+stl+d
lcl|NCBI__GCF_000009985.1:WP_011386526.1 563 AGEEPSED-LRKELVNWVRKEIGPIASPDLIQWSPGLPKTRSGKIMRRILRKIAENDfGSLGDTSTLAD 630
******95.************************************************************ PP
TIGR02188 620 psvveelke 628
p vv++l++
lcl|NCBI__GCF_000009985.1:WP_011386526.1 631 PGVVDDLID 639
*****9975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (629 nodes)
Target sequences: 1 (645 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: 7.65
//
[ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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