Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009493644.1 MICLODRAFT_RS29080 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000262405.1:WP_009493644.1 Length = 652 Score = 914 bits (2363), Expect = 0.0 Identities = 421/640 (65%), Positives = 517/640 (80%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 + +PA R ++ Y A Y+ S+ P+ FW E+ K +DW K ++KNT+F P NV+ Sbjct: 6 YDVPAEWRHRAYLDDAGYRAKYEASVKDPEAFWAEEAKRIDWFKAPTRIKNTNFGPDNVA 65 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126 I+W+EDG N+A NC+DRHL GD+ AIIWEGDD S+SK I+Y+ELH +VCR AN + Sbjct: 66 IRWFEDGVTNVAHNCIDRHLHTRGDQVAIIWEGDDPSESKKITYRELHDEVCRMANIMRN 125 Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186 G+ KGD V IYMPM+PEAA AMLACAR+GA+HSV+FGGFSP+++A RI D+ S ++T+ Sbjct: 126 RGVAKGDRVTIYMPMIPEAAYAMLACARLGAIHSVVFGGFSPDSLASRIQDAKSAFIVTA 185 Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246 DEG+R GR +PLK NVD AL+ V+HV+V++RTG ++ GRD+++H+ E SD Sbjct: 186 DEGLRGGRKVPLKVNVDAALERVGAGVVDHVLVVRRTGSPVNMVPGRDVYYHEAAELVSD 245 Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306 + EEMNAEDPLFILYTSGSTG PKGVLHTTGGYLVYA++T +YVFDYH GD+YWCTAD Sbjct: 246 ECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYASMTHQYVFDYHDGDVYWCTAD 305 Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366 VGWVTGHSY+LYGPLA GATTLMFEGVP +PT +R V+DKHQVNI YTAPTAIR+LM Sbjct: 306 VGWVTGHSYILYGPLANGATTLMFEGVPTYPTISRFWDVIDKHQVNIFYTAPTAIRSLMQ 365 Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426 G++ ++ T R SLR+LGSVGEPINPEAWEWY + +G+ +CP+VDTWWQTETGG +ITPL Sbjct: 366 AGEEPVKKTSRKSLRLLGSVGEPINPEAWEWYHRVVGDGRCPIVDTWWQTETGGILITPL 425 Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486 PGAT+LK GSATRPFFGV+P +VD +G LEGATEG+LVI DSWPGQ RT++GDHERF Q Sbjct: 426 PGATKLKPGSATRPFFGVKPQIVDADGKVLEGATEGNLVIADSWPGQMRTVYGDHERFVQ 485 Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546 TYFST+ YF+GDG RRD+DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAHPK++EAA Sbjct: 486 TYFSTYPGKYFTGDGCRRDQDGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVSEAA 545 Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606 VVG PH+IKGQ IYAYVTL GEEPS EL E+ WVRKEIGP+A+PD++ + LPKTR Sbjct: 546 VVGYPHDIKGQGIYAYVTLMAGEEPSEELRKELVAWVRKEIGPIASPDLIQFAPGLPKTR 605 Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 SGKIMRRILRKIA + +LGDTSTLADPGVV+ L+ +Q Sbjct: 606 SGKIMRRILRKIAEDEFGSLGDTSTLADPGVVDDLITNRQ 645 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: 1461 Number of extensions: 48 Number of successful extensions: 1 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: 652 Length adjustment: 38 Effective length of query: 614 Effective length of database: 614 Effective search space: 376996 Effective search space used: 376996 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_009493644.1 MICLODRAFT_RS29080 (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.1859544.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 1033.2 0.0 0 1032.8 0.0 1.0 1 NCBI__GCF_000262405.1:WP_009493644.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000262405.1:WP_009493644.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1032.8 0.0 0 0 6 628 .. 22 642 .. 18 643 .. 0.98 Alignments for each domain: == domain 1 score: 1032.8 bits; conditional E-value: 0 TIGR02188 6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 y++ ye +++dpe+fwa++ak+ ++w+k ++++++++ p ++Wfedg +nv+ nc+drh+++r d+va NCBI__GCF_000262405.1:WP_009493644.1 22 GYRAKYEASVKDPEAFWAEEAKR-IDWFKAPTRIKNTNFGPdnvAIRWFEDGVTNVAHNCIDRHLHTRGDQVA 93 59999*****************5.**************98877789*************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 iiwegd+++e s+k+tY+el++evcr+an++++ Gv kgdrv+iY+pmipea++amlacaR+Ga+hsvvf+Gf NCBI__GCF_000262405.1:WP_009493644.1 94 IIWEGDDPSE-SKKITYRELHDEVCRMANIMRNRGVAKGDRVTIYMPMIPEAAYAMLACARLGAIHSVVFGGF 165 ********96.************************************************************** PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220 s+++la+Ri+da++ +++tadeglRgg++++lk +vd+ale++ + v++vlvv+rtg++v+ ++ grDv+++ NCBI__GCF_000262405.1:WP_009493644.1 166 SPDSLASRIQDAKSAFIVTADEGLRGGRKVPLKVNVDAALERVGAgVVDHVLVVRRTGSPVN-MVPGRDVYYH 237 *******************************************9999*************66.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 e+ e +s+ec++e++++edplfiLYtsGstG+PkGvlhttgGyl++a++t++yvfd++d+d++wCtaDvGWv NCBI__GCF_000262405.1:WP_009493644.1 238 EAAE-LVSDECPCEEMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYASMTHQYVFDYHDGDVYWCTADVGWV 309 ****.5******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGhsYi+ygPLanGattl+fegvptyp+ srfw+vi+k++v+ifYtaPtaiR+lm++gee vkk++++slr+l NCBI__GCF_000262405.1:WP_009493644.1 310 TGHSYILYGPLANGATTLMFEGVPTYPTISRFWDVIDKHQVNIFYTAPTAIRSLMQAGEEPVKKTSRKSLRLL 382 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 gsvGepinpeaweWy++vvG+++cpivdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd +gk NCBI__GCF_000262405.1:WP_009493644.1 383 GSVGEPINPEAWEWYHRVVGDGRCPIVDTWWQTETGGILITPLPG-ATKLKPGSATRPFFGVKPQIVDADGKV 454 *********************************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512 +e +e g Lvi ++wP+++rt+ygd+erfv+tYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+ NCBI__GCF_000262405.1:WP_009493644.1 455 LEGATE-GNLVIADSWPGQMRTVYGDHERFVQTYFSTYPGKYFTGDGCRRDQDGYYWITGRVDDVINVSGHRM 526 **8777.79**************************************************************** PP TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585 gtae+esalv+h++v+eaavvg+p++ikg+ i+a+v+l++g+e++ee l+kel ++vrkeigpia+pd i+++ NCBI__GCF_000262405.1:WP_009493644.1 527 GTAEVESALVAHPKVSEAAVVGYPHDIKGQGIYAYVTLMAGEEPSEE-LRKELVAWVRKEIGPIASPDLIQFA 598 **********************************************5.************************* PP TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 + lPktRsGkimRR+lrkiae+e +lgd+stl+dp vv++l++ NCBI__GCF_000262405.1:WP_009493644.1 599 PGLPKTRSGKIMRRILRKIAEDEfGSLGDTSTLADPGVVDDLIT 642 ****************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (652 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 21.12 // [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