Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate CA265_RS16340 CA265_RS16340 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Pedo557:CA265_RS16340 Length = 631 Score = 733 bits (1891), Expect = 0.0 Identities = 360/625 (57%), Positives = 455/625 (72%), Gaps = 10/625 (1%) Query: 22 QQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81 +QYE Y++S+ P+ FWGE + W KP+ KV + +F N IKW+E LN+ NC Sbjct: 7 KQYEEDYKKSVENPEQFWGEVAQNFQWRKPWFKVLSWNFNEPN--IKWFEGAKLNITENC 64 Query: 82 LDRHLQENGDRTAIIWEGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMP 140 LDRHL NGD+ AI+WE ++ + S +YK LH VCRFAN L G KKGD + IYMP Sbjct: 65 LDRHLATNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRNGAKKGDRICIYMP 124 Query: 141 MVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKK 200 MVPE A+A+LACARIGAVHSVIFGGFS +++A RI DS ++VIT+D R + IPLK Sbjct: 125 MVPELAIAVLACARIGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSYRGNKQIPLKD 184 Query: 201 NVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLF 260 +DDAL +VE +VL + +GRD+WW D V+ +D +AEEM+AED LF Sbjct: 185 VIDDALIG--CPTVEKCIVLTHIRTPVSMLKGRDVWWEDEVKHVNDICEAEEMDAEDMLF 242 Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320 ILYTSGSTGKPKGV+HT GGY+VYA TF VF+Y PG++Y+CTAD+GW+TGHSY++YGP Sbjct: 243 ILYTSGSTGKPKGVVHTCGGYMVYAGYTFSNVFNYQPGEVYFCTADIGWITGHSYIVYGP 302 Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380 L+ GAT+++FEG+P +PTP+R +V+KH+VN LYTAPTAIR+LM+ GD + G D SS+ Sbjct: 303 LSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTAPTAIRSLMSYGDDPLNGKDLSSI 362 Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440 R+LGSVGEPIN EAW W+ +KIG+ K P+VDTWWQTETGG MI+P+ T K AT P Sbjct: 363 RVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISPIATVTPTKPSFATLP 422 Query: 441 FFGVQPALVDNEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSG 499 G+QP LVD GN +EG G+L I WPG RT +GDHER +QTYFST+ N+YF+G Sbjct: 423 LPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQTYFSTYDNLYFTG 482 Query: 500 DGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAI 559 DG RDEDGYY ITGRVDDVLNVSGHR+GTAE+E+A+ H + E+AVVG PH++KGQ I Sbjct: 483 DGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAVVGYPHDVKGQGI 542 Query: 560 YAYVTL--NHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617 YA+V HGE + ++ V + IG +A PD + + LPKTRSGKIMRRILRK Sbjct: 543 YAFVIYPEMHGEAELSK--KDILQTVTRVIGAIAKPDKILFVSGLPKTRSGKIMRRILRK 600 Query: 618 IAAGDTSNLGDTSTLADPGVVEKLL 642 IA GDTSNLGDTSTL DPGVVE+++ Sbjct: 601 IAEGDTSNLGDTSTLLDPGVVEEII 625 Lambda K H 0.317 0.135 0.421 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: 1327 Number of extensions: 59 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: 631 Length adjustment: 38 Effective length of query: 614 Effective length of database: 593 Effective search space: 364102 Effective search space used: 364102 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 CA265_RS16340 CA265_RS16340 (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.32661.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-291 953.5 0.0 2.6e-291 953.3 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS16340 CA265_RS16340 acetate--CoA ligas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS16340 CA265_RS16340 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 953.3 0.0 2.6e-291 2.6e-291 2 628 .. 4 626 .. 3 627 .. 0.98 Alignments for each domain: == domain 1 score: 953.3 bits; conditional E-value: 2.6e-291 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhve 68 ++ ++y+e y++++e+pe+fw++ a+ +++w kp+ kvl++++++ ++kWfe+++ln++ nc+drh++ lcl|FitnessBrowser__Pedo557:CA265_RS16340 4 TSFKQYEEDYKKSVENPEQFWGEVAQ-NFQWRKPWFKVLSWNFNEpNIKWFEGAKLNITENCLDRHLA 70 5789*********************9.5**************9888********************** PP TIGR02188 69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaR 136 ++ dk ai+we ++++e+s ++tY+ l+++vcr+anvlk+ G kkgdr++iY+pm+pe++ia+lacaR lcl|FitnessBrowser__Pedo557:CA265_RS16340 71 TNGDKPAIVWEPNNPEEESVTYTYKMLHERVCRFANVLKRNGAKKGDRICIYMPMVPELAIAVLACAR 138 ******************************************************************** PP TIGR02188 137 iGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrt 204 iGavhsv+f+Gfsa+++a+Ri+d+++k+vitad+++Rg+k+i+lk+++d+al ++ +vek++v+ ++ lcl|FitnessBrowser__Pedo557:CA265_RS16340 139 IGAVHSVIFGGFSAKSIADRINDSKCKVVITADGSYRGNKQIPLKDVIDDALIGCP-TVEKCIVLTHI 205 *******************************************************9.7********** PP TIGR02188 205 geevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltv 272 ++v+ + +grDvwwe++v++ +++ ce+e++d+ed+lfiLYtsGstGkPkGv+ht gGy+++a +t+ lcl|FitnessBrowser__Pedo557:CA265_RS16340 206 RTPVS-MLKGRDVWWEDEVKH-VNDICEAEEMDAEDMLFILYTSGSTGKPKGVVHTCGGYMVYAGYTF 271 ***76.**************6.********************************************** PP TIGR02188 273 kyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYta 340 vf+++++++++CtaD+GW+tGhsYivygPL++Gat++lfeg+ptyp++srfw+++ek+kv+++Yta lcl|FitnessBrowser__Pedo557:CA265_RS16340 272 SNVFNYQPGEVYFCTADIGWITGHSYIVYGPLSQGATSVLFEGIPTYPTPSRFWDIVEKHKVNTLYTA 339 ******************************************************************** PP TIGR02188 341 PtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitp 408 PtaiR+lm +g++ ++ +dlss+rvlgsvGepin eaw+W+ e++G++k+pivdtwWqtetGgi+i+p lcl|FitnessBrowser__Pedo557:CA265_RS16340 340 PTAIRSLMSYGDDPLNGKDLSSIRVLGSVGEPINEEAWHWFDEKIGHGKAPIVDTWWQTETGGIMISP 407 ******************************************************************** PP TIGR02188 409 lpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkk 476 +++ +t++kp+ atlPl+Gi++ +vde+g+e+e + g L+ik pwP+mlrt ygd+er +tYf++ lcl|FitnessBrowser__Pedo557:CA265_RS16340 408 IAT-VTPTKPSFATLPLPGIQPILVDENGNEIEGNGVMGNLCIKFPWPGMLRTTYGDHERCKQTYFST 474 ***.6****************************666669***************************** PP TIGR02188 477 lkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeai 544 +++lyftGDg+ rd+dGy+ i+GRvDdv+nvsGhr+gtae+e+a+ h v e+avvg+p+++kg+ i lcl|FitnessBrowser__Pedo557:CA265_RS16340 475 YDNLYFTGDGCLRDEDGYYRITGRVDDVLNVSGHRIGTAEVENAINMHAGVVESAVVGYPHDVKGQGI 542 ******************************************************************** PP TIGR02188 545 vafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ell 611 +afv+ e + e e +k++ ++v++ ig+iakpdkil+v+ lPktRsGkimRR+lrkiaeg+ ++l lcl|FitnessBrowser__Pedo557:CA265_RS16340 543 YAFVIYPEMHGEAE-LSKKDILQTVTRVIGAIAKPDKILFVSGLPKTRSGKIMRRILRKIAEGDtSNL 609 *****999888777.5899*********************************************99** PP TIGR02188 612 gdvstledpsvveelke 628 gd+stl dp vvee+++ lcl|FitnessBrowser__Pedo557:CA265_RS16340 610 GDTSTLLDPGVVEEIIA 626 **************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (631 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 0.02s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 7.80 // [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