Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf1N1B4_2849 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 Length = 645 Score = 815 bits (2104), Expect = 0.0 Identities = 394/640 (61%), Positives = 476/640 (74%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S +P V + + Y+ +Y+QS+ +P FW EQA R LDW P+ TV++ +D Sbjct: 5 STFPKADAVRRAAQLSQDDYQRLYRQSIEHPSTFWAEQATRFLDWSAPWQTVQR--YDLK 62 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 + WFA G +NVSYNC+DRHL +RGDQIAIIWEGDDP+ES ITY++LH VC+ AN Sbjct: 63 TGEASWFAGGQINVSYNCIDRHLEKRGDQIAIIWEGDDPAESAQITYKKLHHNVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLAC RIGAIHSVVFGGFSP++L RI+D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR GK +PLK NVD AL + ++ VIV +RT G + W + RDIWY ++ Sbjct: 183 ITADEGVRGGKFVPLKQNVDTALQS--CPNVNTVIVVERTQGQVNWVEDRDIWYHQALRD 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GE++WC Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVMHTTGGYLLQAAMTFKYVFDYRDGEIFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP +R +VIDKH V+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPSTSRFWQVIDKHHVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G ++ SLRLLG+VGEPINPEAW+WY+ VG++RC IVDTWWQTETGG++I Sbjct: 361 LMREGPEPLKETSRESLRLLGTVGEPINPEAWEWYFNTVGEQRCTIVDTWWQTETGGIMI 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL +KPG AT+P FGV P L+D G I+GA G L I SWP Q R++YGD R Sbjct: 421 SPLVSTQRVKPGCATQPMFGVQPVLLDEHGKEIKGAGSGILAIKSSWPAQIRSVYGDPKR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 ++TYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A Sbjct: 481 MIETYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E ++ L+ +L V KEIG A PD+IQWAP LP Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGTEPNDELKKQLLAHVSKEIGNFAKPDLIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVQGLID 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: 1349 Number of extensions: 68 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 Pf1N1B4_2849 (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.19963.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__pseudo1_N1B4:Pf1N1B4_2849 Acetyl-coenzyme A synthetase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 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 ! 1033.7 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1033.7 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdr 65 ++++y++ly+++ie+p++fwa++a++ l+w p+++v++ +l++ ++ Wf++g++nvsync+dr lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 20 SQDDYQRLYRQSIEHPSTFWAEQATRFLDWSAPWQTVQRYDLKTgEASWFAGGQINVSYNCIDR 83 5789*************************************9999******************* PP TIGR02188 66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeavi 129 h+ekr d++aiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 84 HLEKRGDQIAIIWEGDDPAE-SAQITYKKLHHNVCRLANVLKSRGVKKGDRVCIYMPMIPEAAY 146 ******************96.******************************************* PP TIGR02188 130 amlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee 193 amlacaRiGa+hsvvf+Gfs+++l++Ri da++++vitadeg+Rggk ++lk++vd al++++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 147 AMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKFVPLKQNVDTALQSCP- 209 **************************************************************9. PP TIGR02188 194 svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGv 257 +v++v+vv+rt+ +v+ w+e+rD+w+++++++ +s++c+pe++d+edplfiLYtsGstGkPkGv lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 210 NVNTVIVVERTQGQVN-WVEDRDIWYHQALRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGV 271 6*************66.**************7.******************************* PP TIGR02188 258 lhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypd 321 +httgGyll+aa+t+kyvfd++d++ifwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 272 MHTTGGYLLQAAMTFKYVFDYRDGEIFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPS 335 **************************************************************** PP TIGR02188 322 asrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385 +srfw+vi+k++v+ifYtaPta+Ralm++g e +k+++++slr+lg+vGepinpeaweWy+++v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 336 TSRFWQVIDKHHVNIFYTAPTALRALMREGPEPLKETSRESLRLLGTVGEPINPEAWEWYFNTV 399 **************************************************************** PP TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449 G+++c+ivdtwWqtetGgi+i+pl + + +kpg+at+P+fG++++++de+gke++ + g+L lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 400 GEQRCTIVDTWWQTETGGIMISPLVS-TQRVKPGCATQPMFGVQPVLLDEHGKEIKGAGS-GIL 461 **************************.6***************************98777.8** PP TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513 +ik++wP+++r++ygd++r++etYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 462 AIKSSWPAQIRSVYGDPKRMIETYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIG 525 **************************************************************** PP TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpia 577 tae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++e l+k+l ++v+keig++a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 526 TAEVESALVLHDSIAEAAVVGYPHDVKGQGIYAFVTPMNGTEPNDE-LKKQLLAHVSKEIGNFA 588 *********************************************5.***************** PP TIGR02188 578 kpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 kpd i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2849 589 KPDLIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVQGLID 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 12.51 // [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