Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 Length = 645 Score = 815 bits (2104), Expect = 0.0 Identities = 400/641 (62%), Positives = 481/641 (75%), Gaps = 7/641 (1%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S +P V + + Y+ +Y+QSV +P FW EQA R LDW P+ TV++ + Sbjct: 5 STFPKADAVRRAAQLSQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTG 64 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 + WFA LNVSYNC+DRHL +RGDQ+AIIWEGDDP++S +ITY++LHE VC+ AN Sbjct: 65 --EASWFAGAQLNVSYNCIDRHLEKRGDQVAIIWEGDDPADSTSITYKKLHENVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP++L RI+D + V Sbjct: 123 LKNRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTN-PETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242 ITADEGVR GK + LK NVD AL + P+ SS V+V +RT G + W + RDI Y+ ++ Sbjct: 183 ITADEGVRGGKVVSLKQNVDKALQSCPDVSS---VLVVERTKGLVNWVEGRDIKYQQALR 239 Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302 A C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ EV+W Sbjct: 240 EASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDDEVFW 299 Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362 CTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP +R +VIDKHKV+I YTAPTA+R Sbjct: 300 CTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDKHKVNIFYTAPTALR 359 Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422 A+M G ++ +S+RLLG+VGEPINPEAW+WY+ VG+ERCPIVDTWWQTETGG++ Sbjct: 360 ALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVGEERCPIVDTWWQTETGGIM 419 Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482 +SPL A +KPG AT+P FGV P L+D G I+GA G L I SWP Q R++Y D Sbjct: 420 LSPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYRDPQ 479 Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542 R VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H + Sbjct: 480 RMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHENI 539 Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602 AEAA VG PHDIKGQGIYV+VT G ET++ L+ EL V KEIG A PD+IQWAP L Sbjct: 540 AEAAAVGYPHDIKGQGIYVFVTPMNGVETNDELKKELLALVSKEIGSFAKPDLIQWAPAL 599 Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 PKTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 600 PKTRSGKIMRRILRKIACNELDNLGDTSTLADPSVVQGLID 640 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: 1339 Number of extensions: 73 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: 651 Length of database: 645 Length adjustment: 38 Effective length of query: 613 Effective length of database: 607 Effective search space: 372091 Effective search space used: 372091 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 PfGW456L13_1517 (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.19240.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 1018.1 0.0 0 1017.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 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 ! 1017.9 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.98 Alignments for each domain: == domain 1 score: 1017.9 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgel 56 ++++y++ly++++e+p++fwa++a++ l+w p+e+v++ +l++ ++ Wf++++l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 20 SQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTgEASWFAGAQL 74 5789*************************************9999********** PP TIGR02188 57 nvsyncvdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGv 111 nvsync+drh+ekr d+vaiiwegd++ ds ++tY++l+++vcrlanvlk+ Gv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 75 NVSYNCIDRHLEKRGDQVAIIWEGDDPA-DSTSITYKKLHENVCRLANVLKNRGV 128 ***************************9.5************************* PP TIGR02188 112 kkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvi 166 kkgdrv+iY+pmipea++amlac+RiGavhsvvf+Gfs+++l++Ri da++++vi lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 129 KKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVI 183 ******************************************************* PP TIGR02188 167 tadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221 tadeg+Rggkv++lk++vd+al++++ +v++vlvv+rt+ v+ w+egrD+++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 184 TADEGVRGGKVVSLKQNVDKALQSCP-DVSSVLVVERTKGLVN-WVEGRDIKYQQ 236 *************************9.6**********99955.*********** PP TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276 ++++ asa+c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 237 ALRE-ASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVL 290 ***6.************************************************** PP TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviek 331 d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw+vi+k lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 291 DYRDDEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDK 345 ******************************************************* PP TIGR02188 332 ykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvG 386 +kv+ifYtaPta+Ralm++g e +k++++ s+r+lg+vGepinpeaweWy+++vG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 346 HKVNIFYTAPTALRALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVG 400 ******************************************************* PP TIGR02188 387 kekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeve 441 +e+cpivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 401 EERCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKEIK 454 *************************.6***************************9 PP TIGR02188 442 eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiw 496 + gvL+ik++wP+++r++y+d++r+v+tYfk ++g+yftGDgarrd+dG++w lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 455 GAGS-GVLAIKSSWPAQIRSVYRDPQRMVDTYFKPYPGYYFTGDGARRDEDGDYW 508 8777.8************************************************* PP TIGR02188 497 ilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551 i+GR+DdvinvsGhr+gtae+esalv he++aeaa+vg+p++ikg+ i++fv+ + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 509 ITGRIDDVINVSGHRIGTAEVESALVLHENIAEAAAVGYPHDIKGQGIYVFVTPM 563 ******************************************************* PP TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606 +gve+++e l+kel +lv+keig++akpd i+++++lPktRsGkimRR+lrkia lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 564 NGVETNDE-LKKELLALVSKEIGSFAKPDLIQWAPALPKTRSGKIMRRILRKIAC 617 ******95.********************************************** PP TIGR02188 607 ge.ellgdvstledpsvveelke 628 +e ++lgd+stl+dpsvv+ l++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 618 NElDNLGDTSTLADPSVVQGLID 640 ******************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (645 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 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 7.63 // [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