Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 Length = 646 Score = 1313 bits (3399), Expect = 0.0 Identities = 637/646 (98%), Positives = 644/646 (99%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 +YPVRPEVAA+TLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV Sbjct: 1 VYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 60 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125 DIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDP+ESRNITYRELHEEVCKFANALR Sbjct: 61 DIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEEVCKFANALR 120 Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185 GQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT Sbjct: 121 GQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 180 Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG Sbjct: 181 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 240 Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPG+VYWCTA Sbjct: 241 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTA 300 Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKV+DKHKV+ILYTAPTAIRAMM Sbjct: 301 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVVDKHKVNILYTAPTAIRAMM 360 Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP Sbjct: 361 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 420 Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV Sbjct: 421 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 480 Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA Sbjct: 481 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 540 Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT Sbjct: 541 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 600 Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 RSGKIMRRILRKIATAEYDGLGDISTLADP VVAHLIETHKTMNVA Sbjct: 601 RSGKIMRRILRKIATAEYDGLGDISTLADPSVVAHLIETHKTMNVA 646 Lambda K H 0.318 0.135 0.418 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: 1717 Number of extensions: 46 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: 651 Length of database: 646 Length adjustment: 38 Effective length of query: 613 Effective length of database: 608 Effective search space: 372704 Effective search space used: 372704 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 Pf6N2E2_5659 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.4286.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 1025.9 0.2 0 1025.7 0.2 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC 6.2.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1025.7 0.2 0 0 3 628 .. 15 638 .. 13 639 .. 0.98 Alignments for each domain: == domain 1 score: 1025.7 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncv 63 + +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++ ++kWf+dg+lnvsync+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 15 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCL 77 5679*********************5.*************99887789**************** PP TIGR02188 64 drhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127 drh+++r d+vaiiwegd++ e sr++tY+el++evc++an+l+ + v++gd v+iY+pmipea lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 78 DRHLAERGDQVAIIWEGDDPAE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEA 140 ********************96.***************************************** PP TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191 v+amlacaRiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 141 VVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDALTNP 204 ***************************************************************9 PP TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkP 254 e+ s++kv+v+krt +++ w++ rD+w+e+l++ a + c+p+++++e+ lfiLYtsGstGkP lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 205 ETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKP 266 998**************76.**************5.**************************** PP TIGR02188 255 kGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvpt 318 kGv+htt+Gyll+aalt++ vfd+k++d++wCtaDvGWvtGhsYivygPLanGattllfegvp+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 267 KGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPN 330 **************************************************************** PP TIGR02188 319 ypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyy 382 ypd r+++v++k+kv+i+YtaPtaiRa+m+ g+++v+ d sslr+lgsvGepinpeaw+Wyy lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 331 YPDITRVAKVVDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYY 394 **************************************************************** PP TIGR02188 383 evvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446 ++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ +e +e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 395 KNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNLIEGAAE- 456 *****************************.6****************************8777. PP TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGh lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 457 GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGH 520 79************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeig 574 r+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeig lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 521 RMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLELKNWVRKEIG 583 *********************************************999.6************** PP TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 pia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dpsvv++l+e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 584 PIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPSVVAHLIE 638 **********************************9****************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (646 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 9.41 // [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