Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_047005978.1 AAW01_RS03860 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_001010925.1:WP_047005978.1 Length = 642 Score = 834 bits (2154), Expect = 0.0 Identities = 402/629 (63%), Positives = 491/629 (78%), Gaps = 9/629 (1%) Query: 21 PEQYETKYKQSINDPDTFWGEQGKI-LDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAA 79 PEQY+ Y++S+ DPD FW EQ K LDW T K S+ P V IKW+ DGTLN+ Sbjct: 18 PEQYDALYERSVQDPDGFWLEQAKERLDWYTAPTKGAEWSYDP--VDIKWFSDGTLNICY 75 Query: 80 NCLDRHLQENGDRTAIIWEGDDT-SQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138 N +DRHL +GD+ A+I+E D + + ++YR+LH++V R AN L +G++KGD V +Y Sbjct: 76 NAVDRHLDTHGDQIALIFEPDSPDAPGRSLTYRQLHKEVTRVANALKAMGVRKGDRVTLY 135 Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198 MPM+ E A+ MLACARIGA+HSV+FGGFSPEA+AGRI+ SR V+ AD+G+R +++PL Sbjct: 136 MPMIVEGALTMLACARIGAIHSVVFGGFSPEALAGRIMACESRFVVCADQGLRGSKTVPL 195 Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQP-EAMNAED 257 K NVD AL V SV+ V+V TG +I+ +GRD W+ D AS + P E MNAED Sbjct: 196 KANVDAALAMQGV-SVDGVLVFDHTGGEIEMVDGRDHWFADF---ASDDECPCEEMNAED 251 Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317 PLFILYTSGSTG PKGVLHTTGGY ++AATTF Y FDY PGDI+WC+AD+GWVTGH+Y+ Sbjct: 252 PLFILYTSGSTGTPKGVLHTTGGYALWAATTFHYTFDYQPGDIFWCSADIGWVTGHTYVT 311 Query: 318 YGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377 YGPL T+L+FEGVPN+P R V+DKH+VN+ YTAPTAIRALM EGD + + Sbjct: 312 YGPLINAGTSLIFEGVPNYPDHGRFWDVIDKHKVNLFYTAPTAIRALMREGDSFVTSRNL 371 Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSA 437 SSLR+LG+VGEPINPEAW WY++ +GK+ CP+VDTWWQTETGG MIT LP A ++K GSA Sbjct: 372 SSLRVLGTVGEPINPEAWRWYYEVVGKKNCPIVDTWWQTETGGHMITTLPYAHDMKPGSA 431 Query: 438 TRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497 +PFFG+QP LVDN+G+ EGATEGNL IT SWPGQART++GDH+RFEQ YFST+ YF Sbjct: 432 GKPFFGIQPLLVDNDGNTLEGATEGNLCITHSWPGQARTVYGDHDRFEQAYFSTYPGRYF 491 Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQ 557 +GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV HPK+AEAAVVG PH IKGQ Sbjct: 492 TGDGCRRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVLHPKVAEAAVVGYPHDIKGQ 551 Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617 IY YVTLN GEE S ELY+E+R VRKEIGP+ATPD L +TD LPKTRSGKIMRRILRK Sbjct: 552 GIYCYVTLNAGEEGSDELYSELRQHVRKEIGPIATPDHLQFTDGLPKTRSGKIMRRILRK 611 Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 IA D +LGDTSTLADP +V++L+E +Q Sbjct: 612 IAENDYGSLGDTSTLADPSLVDRLIEGRQ 640 Lambda K H 0.317 0.135 0.423 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: 1481 Number of extensions: 74 Number of successful extensions: 5 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: 642 Length adjustment: 38 Effective length of query: 614 Effective length of database: 604 Effective search space: 370856 Effective search space used: 370856 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_047005978.1 AAW01_RS03860 (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.63803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-301 985.2 0.0 6.9e-301 985.0 0.0 1.0 1 NCBI__GCF_001010925.1:WP_047005978.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001010925.1:WP_047005978.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 985.0 0.0 6.9e-301 6.9e-301 4 628 .. 18 637 .. 15 638 .. 0.99 Alignments for each domain: == domain 1 score: 985.0 bits; conditional E-value: 6.9e-301 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkva 75 e+y +lye++++dp+ fw ++ake+l+w + +k ++s +p ++kWf+dg+ln++yn+vdrh+ ++ d++a NCBI__GCF_001010925.1:WP_047005978.1 18 PEQYDALYERSVQDPDGFWLEQAKERLDWYTAPTKGAEWSYDPvDIKWFSDGTLNICYNAVDRHLDTHGDQIA 90 689***************************************99***************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 +i+e d+++ r+ltY++l++ev+r+an+lk++Gv+kgdrv++Y+pmi+e +++mlacaRiGa+hsvvf+Gf NCBI__GCF_001010925.1:WP_047005978.1 91 LIFEPDSPDAPGRSLTYRQLHKEVTRVANALKAMGVRKGDRVTLYMPMIVEGALTMLACARIGAIHSVVFGGF 163 *********9*************************************************************** PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221 s+eala Ri+ +e+++v++ad+glRg k+++lk++vd+al+++ sv+ vlv+ +tg e++ +++grD+w+ + NCBI__GCF_001010925.1:WP_047005978.1 164 SPEALAGRIMACESRFVVCADQGLRGSKTVPLKANVDAALAMQGVSVDGVLVFDHTGGEIE-MVDGRDHWFAD 235 ***********************************************************66.*********** PP TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294 ++ +ec++e++++edplfiLYtsGstG+PkGvlhttgGy+l+aa+t++y+fd++++difwC+aD+GWvt NCBI__GCF_001010925.1:WP_047005978.1 236 FASD---DECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYALWAATTFHYTFDYQPGDIFWCSADIGWVT 305 9996...9***************************************************************** PP TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367 Gh+Y+ ygPL+n t+l+fegvp+ypd++rfw+vi+k+kv+ fYtaPtaiRalm++g+++v++++lsslrvlg NCBI__GCF_001010925.1:WP_047005978.1 306 GHTYVTYGPLINAGTSLIFEGVPNYPDHGRFWDVIDKHKVNLFYTAPTAIRALMREGDSFVTSRNLSSLRVLG 378 ************************************************************************* PP TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440 +vGepinpeaw+WyyevvGk++cpivdtwWqtetGg++it+lp a ++kpgsa +P+fGi++ +vd++g+++ NCBI__GCF_001010925.1:WP_047005978.1 379 TVGEPINPEAWRWYYEVVGKKNCPIVDTWWQTETGGHMITTLPY-AHDMKPGSAGKPFFGIQPLLVDNDGNTL 450 ********************************************.6*************************** PP TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513 e +e g L+i+++wP+++rt+ygd++rf ++Yf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+g NCBI__GCF_001010925.1:WP_047005978.1 451 EGATE-GNLCITHSWPGQARTVYGDHDRFEQAYFSTYPGRYFTGDGCRRDEDGYYWITGRVDDVINVSGHRMG 522 *8777.79***************************************************************** PP TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586 tae+esalv h++vaeaavvg+p++ikg+ i+++v+l++g+e ++e l +el+++vrkeigpia+pd++++++ NCBI__GCF_001010925.1:WP_047005978.1 523 TAEVESALVLHPKVAEAAVVGYPHDIKGQGIYCYVTLNAGEEGSDE-LYSELRQHVRKEIGPIATPDHLQFTD 594 ******************************************9995.************************** PP TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 lPktRsGkimRR+lrkiae++ +lgd+stl+dps v++l+e NCBI__GCF_001010925.1:WP_047005978.1 595 GLPKTRSGKIMRRILRKIAENDyGSLGDTSTLADPSLVDRLIE 637 **********************99***************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (642 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 22.74 // [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