Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF1279 PGA1_c12950 acetyl-coenzyme A synthetase Acs
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >FitnessBrowser__Phaeo:GFF1279 Length = 695 Score = 833 bits (2153), Expect = 0.0 Identities = 411/644 (63%), Positives = 477/644 (74%), Gaps = 5/644 (0%) Query: 2 SAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFD 61 S + Y E A + A Y MY S+ +P+GFWR+QA+R+DWIKPFT VK F Sbjct: 47 SDSKAYAPSEETVARAHVNAAQYDEMYAASMQDPEGFWRQQAERIDWIKPFTQVKDVDFT 106 Query: 62 DHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAES-RNITYRELHEQVCKF 120 +V I W+ADGTLNV+ NC+DRHL RGDQ AIIWE D P E+ ++I+Y++LH +VC+ Sbjct: 107 LGNVSINWYADGTLNVAANCIDRHLDTRGDQTAIIWEPDSPDEAAQHISYKQLHTRVCRM 166 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 AN L V +GD V IY+PMIPEA AMLAC RIGAIHS+VF GFSP+ALA R+ C + Sbjct: 167 ANVLETMGVRKGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALAARVNGCDA 226 Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240 KV+ITADE R G+K LK+N D AL + T K +V KRTGG W RD Y ++ Sbjct: 227 KVLITADEAPRGGRKTPLKSNADAALLH--TKDTVKCLVVKRTGGQTTWIDGRDYDYNEM 284 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 A P EM AE+ LFILYTSGSTG+PKGV HTTGGYL YAA+THE FDY G+I Sbjct: 285 ALEADDYSKPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDI 344 Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360 YWCTADVGWVTGH+YIVYGPLANGATTL+FEGVP YPD +R ++ DKHKV YTAPTA Sbjct: 345 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTA 404 Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420 +RA+M QG VE D SSLR LG+VGEPINPEAW WY VG+ +CPIVDTWWQTETG Sbjct: 405 LRALMGQGNEWVEKCDLSSLRTLGTVGEPINPEAWNWYNDIVGKGKCPIVDTWWQTETGG 464 Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVD-NLGNIIEG-VAEGNLVILDSWPGQARTLY 478 LM+PLPGAH KPG+A +PFFGV P ++D G I G EG L I DSWPGQ RT++ Sbjct: 465 HLMTPLPGAHATKPGAAMKPFFGVAPVVLDPQSGEEITGNGVEGVLCIKDSWPGQMRTVW 524 Query: 479 GDHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVA 538 GDH+RF TYF ++G YFTGDG RRD DG +WITGRVDDV+NVSGHRMGTAE+ESA+VA Sbjct: 525 GDHERFEKTYFSDYKGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVA 584 Query: 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQW 598 H VAEAAVVG PH+IKGQGIY YVTL EPS+ L EL+ WVR EIGPIASPDVIQW Sbjct: 585 HAAVAEAAVVGYPHEIKGQGIYCYVTLMNDREPSDELVKELRTWVRTEIGPIASPDVIQW 644 Query: 599 APGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642 APGLPKTRSGKIMRRILRKIA ++ LGD STLADP VV LI Sbjct: 645 APGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPSVVDDLI 688 Lambda K H 0.319 0.136 0.425 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: 1580 Number of extensions: 86 Number of successful extensions: 4 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: 695 Length adjustment: 39 Effective length of query: 612 Effective length of database: 656 Effective search space: 401472 Effective search space used: 401472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate GFF1279 PGA1_c12950 (acetyl-coenzyme A synthetase Acs)
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.27319.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 1013.5 0.2 0 1013.2 0.2 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1279 PGA1_c12950 acetyl-coenzyme A sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1279 PGA1_c12950 acetyl-coenzyme A synthetase Acs # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1013.2 0.2 0 0 3 628 .. 65 689 .. 63 690 .. 0.98 Alignments for each domain: == domain 1 score: 1013.2 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 ++ +y e+y+ +++dpe fw+++a+ +++w+kpf++v+d +++ +++W++dg+lnv++nc+drh+ +r d++a lcl|FitnessBrowser__Phaeo:GFF1279 65 NAAQYDEMYAASMQDPEGFWRQQAE-RIDWIKPFTQVKDVDFTLgnvSINWYADGTLNVAANCIDRHLDTRGDQTA 139 6789********************9.5**************9877789**************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151 iiwe d+++e +++++Y++l+++vcr+anvl+++Gv+kgdrv+iYlpmipea++amlacaRiGa+hs+vfaGfs++ lcl|FitnessBrowser__Phaeo:GFF1279 140 IIWEPDSPDEAAQHISYKQLHTRVCRMANVLETMGVRKGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPD 215 **************************************************************************** PP TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekea 227 ala R++ ++ak++itade+ Rgg++++lk+++d+al +++++v+ +lvvkrtg + ++w +grD+ ++e+ + a lcl|FitnessBrowser__Phaeo:GFF1279 216 ALAARVNGCDAKVLITADEAPRGGRKTPLKSNADAALLHTKDTVK-CLVVKRTGGQ-TTWIDGRDYDYNEMALE-A 288 ****************************************98776.**********.56***********9995.* PP TIGR02188 228 saecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygP 303 +++ +p+++++edplfiLYtsGstG+PkGv+httgGyl++aa+t++++fd++d+di+wCtaDvGWvtGhsYivygP lcl|FitnessBrowser__Phaeo:GFF1279 289 DDYSKPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDIYWCTADVGWVTGHSYIVYGP 364 **************************************************************************** PP TIGR02188 304 LanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeawe 379 LanGattl+fegvptypdasrfw+v++k+kvt+fYtaPta+Ralm +g+e+v+k dlsslr lg+vGepinpeaw+ lcl|FitnessBrowser__Phaeo:GFF1279 365 LANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTALRALMGQGNEWVEKCDLSSLRTLGTVGEPINPEAWN 440 **************************************************************************** PP TIGR02188 380 WyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eegkeveeeeeggvLvikkp 454 Wy++ vGk+kcpivdtwWqtetGg+l+tplpg a ++kpg+a++P+fG+ ++v+d ++g+e++ + +gvL+ik++ lcl|FitnessBrowser__Phaeo:GFF1279 441 WYNDIVGKGKCPIVDTWWQTETGGHLMTPLPG-AHATKPGAAMKPFFGVAPVVLDpQSGEEITGNGVEGVLCIKDS 515 ********************************.6*********************999*****555559******* PP TIGR02188 455 wPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaea 530 wP+++rt++gd+erf +tYf+++kg+yftGDg+rrd+dG++wi+GRvDdvinvsGhr+gtae+esalv+h avaea lcl|FitnessBrowser__Phaeo:GFF1279 516 WPGQMRTVWGDHERFEKTYFSDYKGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVAHAAVAEA 591 **************************************************************************** PP TIGR02188 531 avvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606 avvg+p+eikg+ i+++v+l++ +e+++e l kel+++vr+eigpia+pd i++++ lPktRsGkimRR+lrkiae lcl|FitnessBrowser__Phaeo:GFF1279 592 AVVGYPHEIKGQGIYCYVTLMNDREPSDE-LVKELRTWVRTEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAE 666 ****************************5.********************************************** PP TIGR02188 607 ge.ellgdvstledpsvveelke 628 ++ +lgd+stl+dpsvv++l++ lcl|FitnessBrowser__Phaeo:GFF1279 667 NDfGSLGDTSTLADPSVVDDLIA 689 *******************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (695 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: 13.31 // [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