Align Acetyl-coenzyme A synthetase 1; AcCoA synthetase 1; Acs 1; EC 6.2.1.1; Acetate--CoA ligase 1; Acyl-activating enzyme 1 (uncharacterized)
to candidate WP_079651098.1 B5X82_RS25170 acetate--CoA ligase
Query= curated2:Q88EH6 (653 letters) >NCBI__GCF_900167915.1:WP_079651098.1 Length = 498 Score = 662 bits (1707), Expect = 0.0 Identities = 307/497 (61%), Positives = 386/497 (77%), Gaps = 3/497 (0%) Query: 6 LYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSFDDHHV 65 LYPV E AA +A YKA+Y +S+ + FW EQA+R+DW++ T+ ++SFD+ Sbjct: 4 LYPVPAEWAARAKVTDADYKALYARSIDDAHAFWLEQAKRLDWVRFPTRTNESSFDEADF 63 Query: 66 DIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEH-RNITYRELHEQVCKFANAL 124 +KWFADG +NV++NCLDRHL ERGDQ+AIIWE D P++ R TY+++HE+VC+FAN L Sbjct: 64 QVKWFADGQINVAANCLDRHLAERGDQVAIIWEPDAPTDAPRRFTYKQVHEEVCRFANVL 123 Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184 + Q V +GD VT+Y+PMIPEA A+LACARIGAIHSVVFGGFSPEALAGRI DC S +VI Sbjct: 124 KAQGVKKGDRVTVYLPMIPEAAFALLACARIGAIHSVVFGGFSPEALAGRIQDCDSSIVI 183 Query: 185 TADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDLMKVA 244 TAD G RGG+ PLK NVD A + S++ +IV + TG ++ RDIWY++ K Sbjct: 184 TADCGRRGGKLVPLKTNVDAAAQH--APSLKSVIVIRATGSEVPMQAGRDIWYDEAAKNV 241 Query: 245 SSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEVYWCT 304 + C + M AE+ LFILYTSGSTGKPKGVLHTTGGYL++A+LTHE FDYRPG+VYWC Sbjct: 242 PADCPAETMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLWASLTHEVCFDYRPGQVYWCA 301 Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTAIRAM 364 AD+GWVTGHSYIVYGPLANGATTL++EGVPN+PD +R+ ++VD+H+V I++TAPTA+RA+ Sbjct: 302 ADIGWVTGHSYIVYGPLANGATTLMYEGVPNWPDASRIWQVVDRHQVEIVFTAPTALRAL 361 Query: 365 MAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGGILIS 424 M +G V SL+LLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETG +I+ Sbjct: 362 MRDGDEFVARTSRKSLKLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIA 421 Query: 425 PLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGDHDRF 484 PLPGAT LKPGSATRP FGVVP LVD G +++GA +GNL I SWPGQ R+++GDH RF Sbjct: 422 PLPGATDLKPGSATRPLFGVVPELVDADGKVLEGATDGNLCITRSWPGQMRTVWGDHARF 481 Query: 485 VDTYFKTFRGMYFTGDG 501 TYF T+ G YFTGDG Sbjct: 482 FQTYFSTYPGKYFTGDG 498 Lambda K H 0.319 0.136 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: 1097 Number of extensions: 65 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: 653 Length of database: 498 Length adjustment: 36 Effective length of query: 617 Effective length of database: 462 Effective search space: 285054 Effective search space used: 285054 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: 53 (25.0 bits)
Align candidate WP_079651098.1 B5X82_RS25170 (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.2838469.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-228 746.4 0.0 1.3e-228 746.2 0.0 1.0 1 NCBI__GCF_900167915.1:WP_079651098.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900167915.1:WP_079651098.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 746.2 0.0 1.3e-228 1.3e-228 5 486 .. 20 498 .] 16 498 .] 0.98 Alignments for each domain: == domain 1 score: 746.2 bits; conditional E-value: 1.3e-228 TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 +yk+ly+++i+d ++fw ++ak+ l+w++ +++ ++s+++ +vkWf+dg++nv++nc+drh+++r d+v NCBI__GCF_900167915.1:WP_079651098.1 20 ADYKALYARSIDDAHAFWLEQAKR-LDWVRFPTRTNESSFDEadfQVKWFADGQINVAANCLDRHLAERGDQV 91 68*********************5.***********9999888889*************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 aiiwe d +++ r++tY+++++evcr+anvlk++Gvkkgdrv++Ylpmipea++a+lacaRiGa+hsvvf+G NCBI__GCF_900167915.1:WP_079651098.1 92 AIIWEPDAPTDAPRRFTYKQVHEEVCRFANVLKAQGVKKGDRVTVYLPMIPEAAFALLACARIGAIHSVVFGG 164 **********99************************************************************* PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fs+eala Ri+d+++ +vitad g Rggk ++lk++vd+a ++a+ s+++v+v++ tg+ev ++ grD+w++ NCBI__GCF_900167915.1:WP_079651098.1 165 FSPEALAGRIQDCDSSIVITADCGRRGGKLVPLKTNVDAAAQHAP-SLKSVIVIRATGSEVP-MQAGRDIWYD 235 ********************************************9.7*************66.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 e+ + +++a+c++e++d+edplfiLYtsGstGkPkGvlhttgGyll+a+lt+++ fd+++++++wC+aD+GWv NCBI__GCF_900167915.1:WP_079651098.1 236 EAAK-NVPADCPAETMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLWASLTHEVCFDYRPGQVYWCAADIGWV 307 **99.5******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGhsYivygPLanGattl++egvp++pdasr+w+v+++++v+i +taPta+Ralm+ g+e+v++++++sl++l NCBI__GCF_900167915.1:WP_079651098.1 308 TGHSYIVYGPLANGATTLMYEGVPNWPDASRIWQVVDRHQVEIVFTAPTALRALMRDGDEFVARTSRKSLKLL 380 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 g+vGepinpeaw+Wy+evvG+++cpi+dtwWqtetG+++i+plpg at+lkpgsat+PlfG+ +e+vd +gk NCBI__GCF_900167915.1:WP_079651098.1 381 GTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIAPLPG-ATDLKPGSATRPLFGVVPELVDADGKV 452 *********************************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486 +e ++ g L+i+++wP+++rt++gd+ rf++tYf++++g yftGDg NCBI__GCF_900167915.1:WP_079651098.1 453 LEGATD-GNLCITRSWPGQMRTVWGDHARFFQTYFSTYPGKYFTGDG 498 *98777.79*************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (498 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 29.46 // [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