Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 3607991 Dshi_1399 acetate--CoA ligase (RefSeq)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Dino:3607991 Length = 653 Score = 842 bits (2176), Expect = 0.0 Identities = 401/642 (62%), Positives = 494/642 (76%), Gaps = 5/642 (0%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 +T A+ I+ +Y MY S++ P+ FWGE G+ LDWIKPY KVK+TSFA +V Sbjct: 9 YTPSADFVKNAHIDSSKYSEMYAASVSDPEGFWGEHGRSLDWIKPYTKVKDTSFAHDDVH 68 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLL 125 ++W+EDGTLN+AANC+DRHL GD+TAII+E DD A ++HI+Y+ELHR VC+ +N L Sbjct: 69 VRWFEDGTLNVAANCIDRHLATRGDQTAIIFEPDDPAEPAQHITYRELHRQVCKLSNVLE 128 Query: 126 ELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVIT 185 +LG++KGD V +YMPM+PEAA AMLACARIGA+HS++F GFSP+A++ RI +++RL+IT Sbjct: 129 DLGVRKGDRVILYMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALSARINGADARLLIT 188 Query: 186 SDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS 245 +D R GR PLK N D AL + ++V+KRTGG+ W +GRD +H+L+ +A Sbjct: 189 ADYAPRGGRQTPLKSNADAALLHTR--DDVKMLVVKRTGGQTTWVDGRDFDYHELMLEAD 246 Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305 + E+ AE PLFILYTSGSTG+PKGV+H++GGYL+YAA+T KYVFD H GD+YWCTA Sbjct: 247 EVQHPVEVEAEHPLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTA 306 Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365 DVGWVTGHSY++YGPLA G TT+MFEGVP +P +R QV DKH+V YTAPTAIRALM Sbjct: 307 DVGWVTGHSYIVYGPLANGGTTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALM 366 Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425 A+G + +E D SSLR+LG+VGEPINPEAW WY +G +CP+VDTWWQTETGG ++TP Sbjct: 367 AKGPEFVETCDLSSLRVLGTVGEPINPEAWNWYNDLVGKGRCPIVDTWWQTETGGHLLTP 426 Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNP--LEGATEGSLVITDSWPGQARTLFGDHER 483 LPGA K GSAT PFFGVQP ++D E EG L + DSWPGQ RT++GDHER Sbjct: 427 LPGAIATKPGSATLPFFGVQPVVLDPHSGAEITETECEGVLCLKDSWPGQMRTVYGDHER 486 Query: 484 FEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIA 543 F +TYFS +K YFSGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH K+A Sbjct: 487 FVKTYFSDYKGYYFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVA 546 Query: 544 EAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLP 603 EAAVVG PH+IKGQ IY YVTL +GEEPS EL E+R WVR EIGP+A PD++ W LP Sbjct: 547 EAAVVGYPHDIKGQGIYCYVTLMNGEEPSEELRKELRTWVRTEIGPIAAPDLIQWAPGLP 606 Query: 604 KTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 KTRSGKIMRRILRKIA D LGDTSTLADP VVE L+E + Sbjct: 607 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPSVVEDLIENR 648 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: 1427 Number of extensions: 66 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: 653 Length adjustment: 38 Effective length of query: 614 Effective length of database: 615 Effective search space: 377610 Effective search space used: 377610 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 3607991 Dshi_1399 (acetate--CoA ligase (RefSeq))
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.8005.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 1010.8 0.0 0 1010.5 0.0 1.0 1 lcl|FitnessBrowser__Dino:3607991 Dshi_1399 acetate--CoA ligase (R Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607991 Dshi_1399 acetate--CoA ligase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1010.5 0.0 0 0 4 628 .. 23 646 .. 20 647 .. 0.98 Alignments for each domain: == domain 1 score: 1010.5 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 ++y+e+y+ +++dpe fw+++++ +l+w+kp++kv+d+s+++ +v+Wfedg+lnv++nc+drh+++r d++aii lcl|FitnessBrowser__Dino:3607991 23 SSKYSEMYAASVSDPEGFWGEHGR-SLDWIKPYTKVKDTSFAHddvHVRWFEDGTLNVAANCIDRHLATRGDQTAII 98 679*********************.6**************99888899***************************** PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeala 154 +e d++ e ++++tY+el+r+vc+l+nvl++lGv+kgdrv++Y+pmipea++amlacaRiGa+hs+vfaGfs++al lcl|FitnessBrowser__Dino:3607991 99 FEPDDPAEPAQHITYRELHRQVCKLSNVLEDLGVRKGDRVILYMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALS 175 ***************************************************************************** PP TIGR02188 155 eRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeasaec 231 Ri+ a+a+l+itad + Rgg++++lk+++d+al ++ ++v+ +lvvkrtg + ++w++grD+ ++el+ + a++ lcl|FitnessBrowser__Dino:3607991 176 ARINGADARLLITADYAPRGGRQTPLKSNADAALLHTRDDVK-MLVVKRTGGQ-TTWVDGRDFDYHELMLE-ADEVQ 249 *************************************99997.899*******.56**************6.99999 PP TIGR02188 232 epekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGa 308 +p ++++e+plfiLYtsGstG+PkGv+h++gGyll+aa+t+kyvfd++++d++wCtaDvGWvtGhsYivygPLanG lcl|FitnessBrowser__Dino:3607991 250 HPVEVEAEHPLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTADVGWVTGHSYIVYGPLANGG 326 999************************************************************************** PP TIGR02188 309 ttllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385 tt++fegvptypdasrfw+v++k+kvt+fYtaPtaiRalm++g e+v+ dlsslrvlg+vGepinpeaw+Wy++ v lcl|FitnessBrowser__Dino:3607991 327 TTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALMAKGPEFVETCDLSSLRVLGTVGEPINPEAWNWYNDLV 403 ***************************************************************************** PP TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eegkeveeeeeggvLvikkpwPsmlrt 461 Gk++cpivdtwWqtetGg+l+tplpg a+++kpgsatlP+fG++++v+d ++g e++e+e +gvL++k++wP+++rt lcl|FitnessBrowser__Dino:3607991 404 GKGRCPIVDTWWQTETGGHLLTPLPG-AIATKPGSATLPFFGVQPVVLDpHSGAEITETECEGVLCLKDSWPGQMRT 479 **************************.6*********************999*****99999*************** PP TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538 +ygd+erfv+tYf+++kg+yf+GDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h +vaeaavvg+p++ lcl|FitnessBrowser__Dino:3607991 480 VYGDHERFVKTYFSDYKGYYFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVAEAAVVGYPHD 556 ***************************************************************************** PP TIGR02188 539 ikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdv 614 ikg+ i+++v+l++g+e++ee l+kel+++vr+eigpia+pd i++++ lPktRsGkimRR+lrkiae++ +lgd+ lcl|FitnessBrowser__Dino:3607991 557 IKGQGIYCYVTLMNGEEPSEE-LRKELRTWVRTEIGPIAAPDLIQWAPGLPKTRSGKIMRRILRKIAEDDfGALGDT 632 ********************5.******************************************************* PP TIGR02188 615 stledpsvveelke 628 stl+dpsvve+l+e lcl|FitnessBrowser__Dino:3607991 633 STLADPSVVEDLIE 646 **********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (653 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 8.99 // [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