Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BWI76_RS02095 BWI76_RS02095 acetyl-coenzyme A synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Koxy:BWI76_RS02095 Length = 652 Score = 1271 bits (3289), Expect = 0.0 Identities = 605/652 (92%), Positives = 631/652 (96%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MSQIHKH IPA IA+RCLINP+QY+A YQQS+ PD FWGEQGKILDW+KPY +VKNTSF Sbjct: 1 MSQIHKHPIPATIAERCLINPEQYQAQYQQSVTDPDAFWGEQGKILDWMKPYTRVKNTSF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 APGN+SIKWYEDGTLNLAANCLDRHL E GD+TAI+WEGDDASQSK+I+Y+ELHRDVCRF Sbjct: 61 APGNISIKWYEDGTLNLAANCLDRHLAERGDQTAIVWEGDDASQSKNITYRELHRDVCRF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN LL+LGIKKGDVVAIYMPMVPEAAVAMLACARIGA+HSVIFGGFSPEAVAGRIIDSNS Sbjct: 121 ANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIHSVIFGGFSPEAVAGRIIDSNS 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 RLVIT+DEG+RAGR+IPLKKNVDDALKNPNV S+E+VVVLKRTGGKIDWQEGRDLWW DL Sbjct: 181 RLVITADEGLRAGRAIPLKKNVDDALKNPNVKSIENVVVLKRTGGKIDWQEGRDLWWSDL 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 +E+AS +HQ EEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA TFKYVFDYHPGDI Sbjct: 241 IEKASAEHQPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAASTFKYVFDYHPGDI 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARM QVVDKHQVNILYTAPTA Sbjct: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPV+DTWWQTETGG Sbjct: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 FMITPLPGA ELKAGSATRPFFGVQP LVDNEG PLEGATEG+L I DSWPGQARTLFGD Sbjct: 421 FMITPLPGAIELKAGSATRPFFGVQPVLVDNEGTPLEGATEGNLAIADSWPGQARTLFGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALV+HP Sbjct: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVSHP 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEP+PELYAEVRNWVRKEIGPLATPDVLHWTD Sbjct: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPELYAEVRNWVRKEIGPLATPDVLHWTD 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS Sbjct: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652 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: 1692 Number of extensions: 52 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 BWI76_RS02095 BWI76_RS02095 (acetyl-coenzyme A synthetase)
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.3295.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 1033.9 0.0 0 1033.7 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS02095 BWI76_RS02095 acetyl-coenzyme A Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS02095 BWI76_RS02095 acetyl-coenzyme A synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1033.7 0.0 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1033.7 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekr 70 + e+y++ y+++++dp++fw++++k l+w+kp+++v+++s++p ++kW+edg+ln+++nc+drh+++r lcl|FitnessBrowser__Koxy:BWI76_RS02095 20 NPEQYQAQYQQSVTDPDAFWGEQGK-ILDWMKPYTRVKNTSFAPgniSIKWYEDGTLNLAANCLDRHLAER 89 679**********************.6****************99899*********************** PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavh 141 d++ai+wegd++++ s+++tY+el+r+vcr+anvl +lG+kkgd vaiY+pm+pea++amlacaRiGa+h lcl|FitnessBrowser__Koxy:BWI76_RS02095 90 GDQTAIVWEGDDASQ-SKNITYRELHRDVCRFANVLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAIH 159 ***********9996.******************************************************* PP TIGR02188 142 svvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaew 211 sv+f+Gfs+ea+a Ri+d++++lvitadeglR g++i+lkk+vd+al++ + s+e+v+v+krtg ++ w lcl|FitnessBrowser__Koxy:BWI76_RS02095 160 SVIFGGFSPEAVAGRIIDSNSRLVITADEGLRAGRAIPLKKNVDDALKNPNVkSIENVVVLKRTGGKID-W 229 *************************************************99889*************66.* PP TIGR02188 212 kegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikded 282 +egrD+ww++l+ek asae++pe++++edplfiLYtsGstGkPkGvlhttgGyl++aa t+kyvfd++++d lcl|FitnessBrowser__Koxy:BWI76_RS02095 230 QEGRDLWWSDLIEK-ASAEHQPEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAASTFKYVFDYHPGD 299 *************7.******************************************************** PP TIGR02188 283 ifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee 353 i+wCtaDvGWvtGhsY++ygPLa+Gattl+fegvp++p+++r+++v++k++v+i+YtaPtaiRalm++g++ lcl|FitnessBrowser__Koxy:BWI76_RS02095 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDK 370 *********************************************************************** PP TIGR02188 354 lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlP 424 +++ +d+sslr+lgsvGepinpeaweWy++++G+ekcp++dtwWqtetGg++itplpg a+elk+gsat+P lcl|FitnessBrowser__Koxy:BWI76_RS02095 371 AIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVMDTWWQTETGGFMITPLPG-AIELKAGSATRP 440 **********************************************************.6*********** PP TIGR02188 425 lfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyi 495 +fG+++++vd+eg+++e +e g L+i ++wP+++rt++gd+erf +tYf+++k++yf+GDgarrd+dGy+ lcl|FitnessBrowser__Koxy:BWI76_RS02095 441 FFGVQPVLVDNEGTPLEGATE-GNLAIADSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYY 510 *****************8777.79*********************************************** PP TIGR02188 496 wilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelk 566 wi+GRvDdv+nvsGhrlgtaeiesalvsh+++aeaavvg+p++ikg+ai+a+v+l++g+e++ e l +e++ lcl|FitnessBrowser__Koxy:BWI76_RS02095 511 WITGRVDDVLNVSGHRLGTAEIESALVSHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPTPE-LYAEVR 580 ***************************************************************5.****** PP TIGR02188 567 klvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++vrkeigp+a+pd ++++++lPktRsGkimRR+lrkia+g+ ++lgd+stl+dp vve+l e lcl|FitnessBrowser__Koxy:BWI76_RS02095 581 NWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDtSNLGDTSTLADPGVVEKLLE 643 ******************************************99***************9976 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 10.37 // [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