Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_019387228.1 P735_RS0106600 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_000283015.1:WP_019387228.1 Length = 635 Score = 690 bits (1780), Expect = 0.0 Identities = 343/627 (54%), Positives = 447/627 (71%), Gaps = 9/627 (1%) Query: 22 EQYETKYKQSINDPDTFWGEQGKI-LDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80 E+Y Y++S+ +P+TFW E + W + V + F V KW+E LN+ N Sbjct: 10 EEYYQVYRKSVRNPETFWEEIAEEHFMWRKKWDNVLSWDFTKPEV--KWFEGAKLNITEN 67 Query: 81 CLDRHLQENGDRTAIIWEGDDTSQ-SKHISYRELHRDVCRFANTLLDLGIKKGDVVAIYM 139 C+DRHL GD+TAII+E + + ++HISYRELH VCRFAN L + G+ KGD V IY+ Sbjct: 68 CIDRHLYTRGDKTAIIFEPNSPEEKAQHISYRELHEKVCRFANVLKNNGVGKGDRVCIYL 127 Query: 140 PMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPLK 199 PM+PE AV++LACARIGA+HSV+F GFS A+A RI D ++VIT+D R ++I LK Sbjct: 128 PMIPELAVSVLACARIGAIHSVVFAGFSSTALATRINDCDCKMVITSDGSYRGSKTIDLK 187 Query: 200 KNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQPEAMNAEDPL 259 VDDAL++ V+ V+V KR S+I+ + RD W + L+++A + +PE M+AEDPL Sbjct: 188 GIVDDALED--CPGVDTVLVAKRINSEINMKADRDKWLQPLLDEAHHDCEPEIMDAEDPL 245 Query: 260 FILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYG 319 FILYTSGSTGKPKG++H+T GY+VY A TFK VF Y D+YWCTAD+GW+TGHSY++YG Sbjct: 246 FILYTSGSTGKPKGMVHSTAGYMVYTAYTFKNVFQYREQDVYWCTADIGWITGHSYIVYG 305 Query: 320 PLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSS 379 PL GATT+MFEGVP++P R ++V KH+VN YTAPTAIRAL EG + +E D SS Sbjct: 306 PLCNGATTVMFEGVPSYPDFGRFWEIVAKHKVNQFYTAPTAIRALAKEGVEHLEKHDLSS 365 Query: 380 LRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSATR 439 L++LG+VGEPIN EAW WY +GK+K P+VDTWWQTETGG MITP+ A K AT Sbjct: 366 LKVLGTVGEPINEEAWHWYDDNVGKKKSPIVDTWWQTETGGIMITPIAFATPTKPTYATL 425 Query: 440 PFFGVQPALVDNEGHPQEG-ATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFS 498 PF GVQPAL+D G +G +G L I WP ART++G+H+R++ TYFS ++N YF+ Sbjct: 426 PFIGVQPALMDEHGQEIKGNQVDGRLCIKFPWPSMARTIWGNHQRYKDTYFSAYENKYFT 485 Query: 499 GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQA 558 GDGA RDE GYY ITGRVDDV+ VSGH LGTA IE A+ HP +AE+A+VG PH IKG A Sbjct: 486 GDGALRDEVGYYRITGRVDDVIIVSGHNLGTAPIEDAINEHPAVAESAIVGFPHDIKGNA 545 Query: 559 IYAYVTLNHGEEPSP--ELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616 +Y YVTL E L E+ + ++IGP+A D + +T+ LPKTRSGKIMRRILR Sbjct: 546 LYGYVTLKETGESRDHNNLRKEINQIITEQIGPIAKLDKIQFTNGLPKTRSGKIMRRILR 605 Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLE 643 KIA+ +TSNLGDTSTL +P VV+++++ Sbjct: 606 KIASNETSNLGDTSTLLNPEVVQEIMD 632 Lambda K H 0.317 0.135 0.423 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: 1281 Number of extensions: 61 Number of successful extensions: 6 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: 652 Length of database: 635 Length adjustment: 38 Effective length of query: 614 Effective length of database: 597 Effective search space: 366558 Effective search space used: 366558 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 WP_019387228.1 P735_RS0106600 (acetate--CoA ligase)
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.2849018.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-297 974.1 0.4 1.5e-297 973.9 0.4 1.0 1 NCBI__GCF_000283015.1:WP_019387228.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000283015.1:WP_019387228.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 973.9 0.4 1.5e-297 1.5e-297 2 628 .. 7 632 .. 6 633 .. 0.98 Alignments for each domain: == domain 1 score: 973.9 bits; conditional E-value: 1.5e-297 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdk 73 ++leey ++y++++++pe+fw++ a+e++ w k++++vl++++++ +vkWfe+++ln++ nc+drh+ +r dk NCBI__GCF_000283015.1:WP_019387228.1 7 KHLEEYYQVYRKSVRNPETFWEEIAEEHFMWRKKWDNVLSWDFTKpEVKWFEGAKLNITENCIDRHLYTRGDK 79 6899**************************************9988*************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aii+e ++++e++++++Y+el+++vcr+anvlk+ Gv kgdrv+iYlpmipe+++ +lacaRiGa+hsvvfa NCBI__GCF_000283015.1:WP_019387228.1 80 TAIIFEPNSPEEKAQHISYRELHEKVCRFANVLKNNGVGKGDRVCIYLPMIPELAVSVLACARIGAIHSVVFA 152 ************************************************************************* PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219 Gfs+ ala+Ri+d+++k+vit+d+++Rg k+i+lk ivd+ale+++ v++vlv kr+++e++ +k +rD+w+ NCBI__GCF_000283015.1:WP_019387228.1 153 GFSSTALATRINDCDCKMVITSDGSYRGSKTIDLKGIVDDALEDCP-GVDTVLVAKRINSEIN-MKADRDKWL 223 *********************************************9.6*************66.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 + l+++ a+++cepe +d+edplfiLYtsGstGkPkG++h+t+Gy++++a+t+k vf+++++d++wCtaD+GW NCBI__GCF_000283015.1:WP_019387228.1 224 QPLLDE-AHHDCEPEIMDAEDPLFILYTSGSTGKPKGMVHSTAGYMVYTAYTFKNVFQYREQDVYWCTADIGW 295 *****6.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 +tGhsYivygPL+nGatt++fegvp+ypd +rfwe++ k+kv++fYtaPtaiRal k+g e+++khdlssl+v NCBI__GCF_000283015.1:WP_019387228.1 296 ITGHSYIVYGPLCNGATTVMFEGVPSYPDFGRFWEIVAKHKVNQFYTAPTAIRALAKEGVEHLEKHDLSSLKV 368 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lg+vGepin eaw+Wy ++vGk+k+pivdtwWqtetGgi+itp++ at++kp atlP++G++++++de+g+ NCBI__GCF_000283015.1:WP_019387228.1 369 LGTVGEPINEEAWHWYDDNVGKKKSPIVDTWWQTETGGIMITPIAF-ATPTKPTYATLPFIGVQPALMDEHGQ 440 *********************************************9.6************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 e++ ++ +g L+ik pwPsm+rti+g+++r+ +tYf+++++ yftGDga rd+ Gy+ i+GRvDdvi vsGh+ NCBI__GCF_000283015.1:WP_019387228.1 441 EIKGNQVDGRLCIKFPWPSMARTIWGNHQRYKDTYFSAYENKYFTGDGALRDEVGYYRITGRVDDVIIVSGHN 513 ***88888***************************************************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegve.edeeelekelkklvrkeigpiakpdkil 583 lgta ie+a+ +h+avae+a+vg+p++ikg+a++ +v+lke+ e d+++l+ke++++++++igpiak dki+ NCBI__GCF_000283015.1:WP_019387228.1 514 LGTAPIEDAINEHPAVAESAIVGFPHDIKGNALYGYVTLKETGEsRDHNNLRKEINQIITEQIGPIAKLDKIQ 586 ****************************************9877245569*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkia++e ++lgd+stl +p+vv+e+++ NCBI__GCF_000283015.1:WP_019387228.1 587 FTNGLPKTRSGKIMRRILRKIASNEtSNLGDTSTLLNPEVVQEIMD 632 *************************99****************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (635 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 22.81 // [ok]
This GapMind analysis is from Sep 24 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