Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__azobra:AZOBR_RS00270 Length = 646 Score = 936 bits (2420), Expect = 0.0 Identities = 443/643 (68%), Positives = 516/643 (80%), Gaps = 3/643 (0%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS S +PV+ E+A + DEA Y +Y+QS+ +P+ FW EQ KR+DWIKP++ VK S+ Sbjct: 1 MSDNSFFPVKQEIAKTAYVDEAAYARLYEQSINDPEAFWGEQGKRIDWIKPYSKVKDVSY 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 V IKWF DGTLNVS NC+DRHLA RGDQ AII+EGDDP S++ITY+ELHE+VC+ Sbjct: 61 TGD-VHIKWFYDGTLNVSANCVDRHLATRGDQTAIIFEGDDPGVSKHITYKELHEQVCRL 119 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 AN L+ V +GD VTIY+PMIPEA AMLAC R+GAIHS+VFGGFSP++L RI+DC S Sbjct: 120 ANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGGFSPDSLKDRIVDCDS 179 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 VIT+DEG+R G+K+PLKAN D A+ ++ V+V K T GN+ W + RD+WY + Sbjct: 180 HFVITSDEGLRGGRKVPLKANADKAVA--AAPGVKHVLVVKHTGGNVAWTEGRDLWYHEE 237 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 + C P+EM AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDYK GEV Sbjct: 238 IASVSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEV 297 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGWVTGHSYIVYGPLANGATTL+FEGVP YPDI+R +V+DKHKV+I YTAPTA Sbjct: 298 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTA 357 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IR++M G V+ SSLR+LGSVGEPINPEAW WYY VG RCPIVDTWWQTETGG Sbjct: 358 IRSLMREGEGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGG 417 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LI+PLPGA KPGSAT+PFFGV P +VDN G +EG EGNL I DSWPGQ RT++GD Sbjct: 418 ILITPLPGAIGQKPGSATKPFFGVKPVVVDNDGKELEGETEGNLCIADSWPGQMRTVFGD 477 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H+RFV TYF TF+G YFTGDG RRD DGYYWITGRVDDV+NVSGHRMGTAE+ESA+VAHP Sbjct: 478 HERFVQTYFSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHP 537 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVG PHD+KGQGIY YVTLNAGE +E LR EL WVRKEIGPIASPD+IQW+P Sbjct: 538 KVAEAAVVGYPHDLKGQGIYAYVTLNAGESPTEELRKELVAWVRKEIGPIASPDLIQWSP 597 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 GLPKTRSGKIMRRILRKIA E+D LGD STLADP VV LIE Sbjct: 598 GLPKTRSGKIMRRILRKIAANEHDSLGDTSTLADPTVVTDLIE 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: 1472 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: 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 AZOBR_RS00270 AZOBR_RS00270 (acetyl-CoA synthetase)
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.8281.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 1052.7 0.0 0 1052.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1052.5 0.0 0 0 4 628 .. 21 640 .. 18 641 .. 0.98 Alignments for each domain: == domain 1 score: 1052.5 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekr 70 +y++lye++i+dpe+fw++++k +++w+kp++kv+d s + ++kWf dg+lnvs+ncvdrh+++r lcl|FitnessBrowser__azobra:AZOBR_RS00270 21 EAAYARLYEQSINDPEAFWGEQGK-RIDWIKPYSKVKDVSYTGdvHIKWFYDGTLNVSANCVDRHLATR 88 578*********************.5*************9987779*********************** PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139 d++aii+egd++g s+++tY+el+++vcrlanvlk+ Gvkkgdrv+iYlpmipea++amlacaR+Ga lcl|FitnessBrowser__azobra:AZOBR_RS00270 89 GDQTAIIFEGDDPGV-SKHITYKELHEQVCRLANVLKKNGVKKGDRVTIYLPMIPEAAYAMLACARVGA 156 **************7.***************************************************** PP TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeev 208 +hs+vf+Gfs+++l++Rivd+++++vit+deglRgg++++lk+++d+a+++a+ v++vlvvk+tg +v lcl|FitnessBrowser__azobra:AZOBR_RS00270 157 IHSIVFGGFSPDSLKDRIVDCDSHFVITSDEGLRGGRKVPLKANADKAVAAAP-GVKHVLVVKHTGGNV 224 ****************************************************9.6*************7 PP TIGR02188 209 aewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfd 277 a w+egrD+w++e++++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd lcl|FitnessBrowser__azobra:AZOBR_RS00270 225 A-WTEGRDLWYHEEIAS-VSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFD 291 7.**************6.*************************************************** PP TIGR02188 278 ikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRa 346 +kd++++wCtaDvGWvtGhsYivygPLanGattl+fegvptypd srfw+v++k+kv+ifYtaPtaiR+ lcl|FitnessBrowser__azobra:AZOBR_RS00270 292 YKDGEVYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTAIRS 360 ********************************************************************* PP TIGR02188 347 lmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415 lm++ge vkk+++sslr+lgsvGepinpeaw Wyy+vvG+++cpivdtwWqtetGgilitplpg a+ lcl|FitnessBrowser__azobra:AZOBR_RS00270 361 LMREGEGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGGILITPLPG-AIG 428 *****************************************************************.6** PP TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484 +kpgsat+P+fG++++vvd++gke+e e+e g L+i ++wP+++rt++gd+erfv+tYf+++ g+yftG lcl|FitnessBrowser__azobra:AZOBR_RS00270 429 QKPGSATKPFFGVKPVVVDNDGKELEGETE-GNLCIADSWPGQMRTVFGDHERFVQTYFSTFAGYYFTG 496 **************************8887.79************************************ PP TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkeg 553 Dg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalv+h++vaeaavvg+p+++kg+ i+a+v+l++g lcl|FitnessBrowser__azobra:AZOBR_RS00270 497 DGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVVGYPHDLKGQGIYAYVTLNAG 565 ********************************************************************* PP TIGR02188 554 veedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledps 621 ++++ee l+kel ++vrkeigpia+pd i++ + lPktRsGkimRR+lrkia++e ++lgd+stl+dp+ lcl|FitnessBrowser__azobra:AZOBR_RS00270 566 ESPTEE-LRKELVAWVRKEIGPIASPDLIQWSPGLPKTRSGKIMRRILRKIAANEhDSLGDTSTLADPT 633 ***995.************************************************99************ PP TIGR02188 622 vveelke 628 vv +l+e lcl|FitnessBrowser__azobra:AZOBR_RS00270 634 VVTDLIE 640 **99986 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 8.93 // [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