Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_5149 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 Length = 645 Score = 828 bits (2138), Expect = 0.0 Identities = 401/640 (62%), Positives = 478/640 (74%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S YP V + + YK +Y++S+ +P FW EQA R LDW+ P+ TV++ +D Sbjct: 5 SQYPQADAVRRAAQLSQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQR--YDLK 62 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 + D WFA G LNVS NCLDRHL RGDQ AIIWEGDDP+ES ITY++LH VC+ AN Sbjct: 63 NGDATWFAGGKLNVSANCLDRHLQTRGDQTAIIWEGDDPAESAEITYKKLHNHVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP++L RI+D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR G+ +PLK NVD AL + ++ V+V +RT G + W + RD+WY M Sbjct: 183 ITADEGVRGGRFVPLKRNVDKALES--CPNVSTVLVVERTQGEVNWVEGRDLWYHQAMHE 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ EV+WC Sbjct: 241 MSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP +R +VIDKH+V+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPSSSRFWQVIDKHQVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G ++ SLRLLGSVGEPINPEAW+WY+ VG++RCPIVDTWWQTETGG+++ Sbjct: 361 LMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNTVGEQRCPIVDTWWQTETGGIML 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL A LKPG ATRP FGV P L+D +G I GA G L I SWPGQ R++YGDH R Sbjct: 421 SPLVSAPRLKPGCATRPMFGVQPVLLDEVGKEISGAGSGVLAIKSSWPGQIRSVYGDHQR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A Sbjct: 481 MVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E ++ L+ EL V KEIG A P++IQWAP LP Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGVEANDELKKELLAHVSKEIGSFAKPELIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 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: 1353 Number of extensions: 70 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 Pf6N2E2_5149 (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.17134.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 1030.4 0.0 0 1030.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 Acetyl-coenzyme A synthetase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 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 ! 1030.1 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1030.1 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdr 65 +++eyk+ly+e+ie+p++fwa++a++ l+w++p+++v++ +l++ +++Wf++g+lnvs+nc+dr lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 20 SQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNgDATWFAGGKLNVSANCLDR 83 5799*************************************9999******************* PP TIGR02188 66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeavi 129 h+++r d++aiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 84 HLQTRGDQTAIIWEGDDPAE-SAEITYKKLHNHVCRLANVLKSRGVKKGDRVCIYMPMIPEAAY 146 ******************96.******************************************* PP TIGR02188 130 amlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee 193 amlac+RiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rgg+ ++lk++vd+ale+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 147 AMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFVPLKRNVDKALESCP- 209 **************************************************************9. PP TIGR02188 194 svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGv 257 +v++vlvv+rt+ ev+ w+egrD+w+++++++ s++c+pe++d+edplfiLYtsGstGkPkGv lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 210 NVSTVLVVERTQGEVN-WVEGRDLWYHQAMHE-MSDDCPPEPMDAEDPLFILYTSGSTGKPKGV 271 6*************66.**************6.******************************* PP TIGR02188 258 lhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypd 321 lhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 272 LHTTGGYLLQAAMTFKYVLDYRDNEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPS 335 **************************************************************** PP TIGR02188 322 asrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevv 385 +srfw+vi+k++v+ifYtaPta+Ralm++g +++++++slr+lgsvGepinpeaweWy+++v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 336 SSRFWQVIDKHQVNIFYTAPTALRALMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNTV 399 **************************************************************** PP TIGR02188 386 GkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449 G+++cpivdtwWqtetGgi+++pl + a lkpg+at+P+fG++++++de gke++ + gvL lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 400 GEQRCPIVDTWWQTETGGIMLSPLVS-APRLKPGCATRPMFGVQPVLLDEVGKEISGAGS-GVL 461 **************************.69**************************98777.8** PP TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513 +ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+g lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 462 AIKSSWPGQIRSVYGDHQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIG 525 **************************************************************** PP TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpia 577 tae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++gve+++e l+kel ++v+keig++a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 526 TAEVESALVLHDNIAEAAVVGYPHDLKGQGIYAFVTPMNGVEANDE-LKKELLAHVSKEIGSFA 588 ********************************************95.***************** PP TIGR02188 578 kpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 kp+ i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvve l++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5149 589 KPELIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVEGLID 640 ************************************************9876 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 10.55 // [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