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.15574.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.69 // [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:
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