Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_016556836.1 RGCCGE502_RS24205 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000298315.2:WP_016556836.1 Length = 651 Score = 887 bits (2291), Expect = 0.0 Identities = 421/639 (65%), Positives = 505/639 (79%), Gaps = 9/639 (1%) Query: 13 IADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYED 72 + + LI+ +YE Y++S+ PD FWG+ GK +DW KPY KVKNTSF G VSIKW+ED Sbjct: 12 VKNHALIDKAKYEQWYEESVENPDKFWGKHGKRIDWFKPYTKVKNTSFT-GRVSIKWFED 70 Query: 73 GTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKG 132 G N++ NC+DRHL+ NG++TAII+EGD+ K I+Y EL+ VCR AN + + G+KKG Sbjct: 71 GQTNVSYNCIDRHLKTNGNQTAIIFEGDNPYVDKKITYNELYEHVCRMANVMKKHGVKKG 130 Query: 133 DVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRA 192 D V IYMPM+PEAA AMLACARIGAVHSV+FGGFSPEA+AGRI+D S V+T DEGVR Sbjct: 131 DRVTIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPEALAGRIVDCESTFVVTCDEGVRG 190 Query: 193 GRSIPLKKNVDDALKNPNVTSVEHVVV-----LKRTGGKIDWQEGRDLWWHDLVEQASDQ 247 G+ +PLK N D A+ ++ + +HV+V ++RTGGK W GRDLW+H + + Sbjct: 191 GKPVPLKDNTDTAI---HIAARQHVIVDKVLVVRRTGGKTGWAPGRDLWYHQEIATVKPE 247 Query: 248 HQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADV 307 +M AEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA+T +YVFDYHPGDIYWCTADV Sbjct: 248 CPPVKMRAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHPGDIYWCTADV 307 Query: 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAE 367 GWVTGHSY++YGPLA ATTLMFEGVPN+P R +V+DKH+VNI YTAPTAIR+LM Sbjct: 308 GWVTGHSYIVYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGA 367 Query: 368 GDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLP 427 GD + + RSSLR+LG+VGEPINPEAWEWY+ +G+++CPV+DTWWQTETGG MITPLP Sbjct: 368 GDHFVTRSSRSSLRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLP 427 Query: 428 GATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQT 487 GAT+LK GSAT PFFGV+P LVDNEGN L+GA +G+L I DSWPGQ RT++GDHERF QT Sbjct: 428 GATDLKPGSATTPFFGVKPQLVDNEGNVLQGAADGNLCIIDSWPGQMRTVYGDHERFIQT 487 Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547 YFST+K YF+GDG RRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H ++EAAV Sbjct: 488 YFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSEAAV 547 Query: 548 VGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607 VG PH IKGQ IY YVTL G E S +L ++ VR EIGP+A PD + + LPKTRS Sbjct: 548 VGYPHPIKGQGIYCYVTLMAGNEGSDDLRQQLVKHVRSEIGPIAAPDKIQFAPGLPKTRS 607 Query: 608 GKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 GKIMRRILRKIA D +LGDTSTLADP VV+ L+ +Q Sbjct: 608 GKIMRRILRKIAEDDFGSLGDTSTLADPAVVDDLIANRQ 646 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: 1499 Number of extensions: 55 Number of successful extensions: 3 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: 651 Length adjustment: 38 Effective length of query: 614 Effective length of database: 613 Effective search space: 376382 Effective search space used: 376382 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_016556836.1 RGCCGE502_RS24205 (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.2457888.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 1033.8 0.0 0 1033.6 0.0 1.0 1 NCBI__GCF_000298315.2:WP_016556836.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000298315.2:WP_016556836.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1033.6 0.0 0 0 4 628 .. 20 643 .. 17 644 .. 0.98 Alignments for each domain: == domain 1 score: 1033.6 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkv 74 +y+++yee++e+p+kfw+k++k +++w+kp++kv+++s++ ++kWfedg++nvsync+drh++++ +++ NCBI__GCF_000298315.2:WP_016556836.1 20 KAKYEQWYEESVENPDKFWGKHGK-RIDWFKPYTKVKNTSFTGrvSIKWFEDGQTNVSYNCIDRHLKTNGNQT 91 679*********************.5**************998789*************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 aii+egd++ +k+tY+el+++vcr+anv+k++Gvkkgdrv+iY+pmipea++amlacaRiGavhsvvf+G NCBI__GCF_000298315.2:WP_016556836.1 92 AIIFEGDNPYV-DKKITYNELYEHVCRMANVMKKHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFGG 163 *******9996.9************************************************************ PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrDv 217 fs+eala Rivd+e+ +v+t deg+Rggk ++lk+++d a++ a + v+kvlvv+rtg + + w grD+ NCBI__GCF_000298315.2:WP_016556836.1 164 FSPEALAGRIVDCESTFVVTCDEGVRGGKPVPLKDNTDTAIHIAARqhvIVDKVLVVRRTGGK-TGWAPGRDL 235 ****************************************98766545689************.56******* PP TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290 w+++++++ ++ ec+p k+ +edplfiLYtsGstGkPkGvlhttgGyl++aa+t++yvfd++++di+wCtaDv NCBI__GCF_000298315.2:WP_016556836.1 236 WYHQEIAT-VKPECPPVKMRAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHPGDIYWCTADV 307 *******6.**************************************************************** PP TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363 GWvtGhsYivygPLan attl+fegvp++pd++rfwevi+k+kv+ifYtaPtaiR+lm +g+++v++ ++ssl NCBI__GCF_000298315.2:WP_016556836.1 308 GWVTGHSYIVYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDHFVTRSSRSSL 380 ************************************************************************* PP TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436 r+lg+vGepinpeaweWyy+vvG+++cp++dtwWqtetGg++itplpg at+lkpgsat+P+fG+++++vd+e NCBI__GCF_000298315.2:WP_016556836.1 381 RLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPG-ATDLKPGSATTPFFGVKPQLVDNE 452 ************************************************.6*********************** PP TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509 g+ ++ ++ g L+i ++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvsG NCBI__GCF_000298315.2:WP_016556836.1 453 GNVLQGAAD-GNLCIIDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSG 524 ****98777.79************************************************************* PP TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582 hrlgtae+esalvsh+ v+eaavvg+p+ ikg+ i+++v+l++g+e +++ l+++l k+vr+eigpia+pdki NCBI__GCF_000298315.2:WP_016556836.1 525 HRLGTAEVESALVSHNLVSEAAVVGYPHPIKGQGIYCYVTLMAGNEGSDD-LRQQLVKHVRSEIGPIAAPDKI 596 **********************************************9995.********************** PP TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++++ lPktRsGkimRR+lrkiae++ +lgd+stl+dp+vv++l++ NCBI__GCF_000298315.2:WP_016556836.1 597 QFAPGLPKTRSGKIMRRILRKIAEDDfGSLGDTSTLADPAVVDDLIA 643 *******************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (651 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: 25.18 // [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