Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_034212718.1 N787_RS08655 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000747155.1:WP_034212718.1 Length = 653 Score = 884 bits (2284), Expect = 0.0 Identities = 429/643 (66%), Positives = 500/643 (77%), Gaps = 6/643 (0%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 ++PV A+ A Y +Y S+ +P+ FW + +RL W KP+T K TSF Sbjct: 5 IHPVPAGFEAAAALKRADYDRLYADSLRDPEAFWSQVGRRLQWSKPYTRAKDTSFALEDF 64 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDP-SESRNITYRELHEEVCKFANAL 124 I+W+ADG LNVS NCLDRHLAERGD+ AIIWE DDP + SR I+YRELH +VC+ ANAL Sbjct: 65 HIRWYADGQLNVSVNCLDRHLAERGDKTAIIWEADDPKTPSRRISYRELHADVCRLANAL 124 Query: 125 RGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVI 184 V +GD VT+Y+PMIPEA VAMLAC RIGAIHSVVFGGFSP+++A RI DC SK+VI Sbjct: 125 TALGVVKGDRVTLYLPMIPEAAVAMLACARIGAIHSVVFGGFSPDSIANRIADCASKLVI 184 Query: 185 TADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244 TADEG+R GK IPLKANVD+AL P T++++ V+V + T G + RD WY+ ++ Sbjct: 185 TADEGLRGGKAIPLKANVDEALRKPGTNTVETVLVVRHTGGGVPMQMPRDRWYDAVVSSQ 244 Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304 M AE+ LFILYTSGSTGKPKGV HTT GYL +A+ THE VFD K +V+WCT Sbjct: 245 PATHDAPAMDAEDPLFILYTSGSTGKPKGVLHTTGGYLTWASYTHECVFDLKDDDVFWCT 304 Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364 ADVGWVTGHSY+VYGPLANGATT++FEGVP+YPD R + +DKH+V+I YTAPTAIRA+ Sbjct: 305 ADVGWVTGHSYVVYGPLANGATTVMFEGVPSYPDTGRFWEAVDKHQVTIFYTAPTAIRAL 364 Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424 M G A V+ + S+RLLG+VGEPINPEAW+WY++ VG ERCPIVDTWWQTETGG+LIS Sbjct: 365 MREGDAPVKRSSRKSIRLLGTVGEPINPEAWEWYHRVVGDERCPIVDTWWQTETGGILIS 424 Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484 PLPGA A KPGSAT PFFGV PALVD G +EGA EGNLV+LDSWPGQ RT+YGDH RF Sbjct: 425 PLPGAVATKPGSATLPFFGVQPALVDAEGKRLEGATEGNLVLLDSWPGQMRTVYGDHQRF 484 Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544 +DTYFKT+ G YFTGDG RRD DGYYWITGRVDDV+NVSGHRMGTAE+ESA+V HP VAE Sbjct: 485 IDTYFKTYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVGHPAVAE 544 Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604 AAVVG PHDIKGQGIY YVTL AG E +EALR EL VRK+IGPIA+PD +QWAPGLPK Sbjct: 545 AAVVGAPHDIKGQGIYAYVTLKAGIEPTEALRKELVAHVRKDIGPIAAPDWLQWAPGLPK 604 Query: 605 TRSGKIMRRILRKIATAEYD-----GLGDISTLADPGVVAHLI 642 TRSGKIMRRILRKIA A D GLGD STLADPGVV L+ Sbjct: 605 TRSGKIMRRILRKIAEAGPDGVDRAGLGDTSTLADPGVVDSLV 647 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: 1476 Number of extensions: 66 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: 653 Length adjustment: 38 Effective length of query: 613 Effective length of database: 615 Effective search space: 376995 Effective search space used: 376995 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_034212718.1 N787_RS08655 (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.644365.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-307 1006.8 0.0 2e-307 1006.5 0.0 1.0 1 NCBI__GCF_000747155.1:WP_034212718.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000747155.1:WP_034212718.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1006.5 0.0 2e-307 2e-307 4 628 .. 20 648 .. 17 649 .. 0.97 Alignments for each domain: == domain 1 score: 1006.5 bits; conditional E-value: 2e-307 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 +y +ly+++ +dpe+fw++ ++ +l+w kp+++ +d+s++ +++W++dg+lnvs+nc+drh+++r dk NCBI__GCF_000747155.1:WP_034212718.1 20 RADYDRLYADSLRDPEAFWSQVGR-RLQWSKPYTRAKDTSFALedfHIRWYADGQLNVSVNCLDRHLAERGDK 91 578********************9.5**************9877789************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aiiwe+d++++ sr+++Y+el+++vcrlan+l++lGv kgdrv++Ylpmipea++amlacaRiGa+hsvvf+ NCBI__GCF_000747155.1:WP_034212718.1 92 TAIIWEADDPKTPSRRISYRELHADVCRLANALTALGVVKGDRVTLYLPMIPEAAVAMLACARIGAIHSVVFG 164 ************************************************************************* PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218 Gfs++++a+Ri d+ +klvitadeglRggk+i+lk++vdeal+k + +ve+vlvv++tg v ++ rD w NCBI__GCF_000747155.1:WP_034212718.1 165 GFSPDSIANRIADCASKLVITADEGLRGGKAIPLKANVDEALRKPGTnTVETVLVVRHTGGGVP-MQMPRDRW 236 ********************************************9988**************66.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 ++ +v++ ++a++++ ++d+edplfiLYtsGstGkPkGvlhttgGyl++a++t++ vfd+kd+d+fwCtaDvG NCBI__GCF_000747155.1:WP_034212718.1 237 YDAVVSS-QPATHDAPAMDAEDPLFILYTSGSTGKPKGVLHTTGGYLTWASYTHECVFDLKDDDVFWCTADVG 308 ******6.***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364 WvtGhsY+vygPLanGatt++fegvp+ypd++rfwe ++k++vtifYtaPtaiRalm++g++ vk+ +++s+r NCBI__GCF_000747155.1:WP_034212718.1 309 WVTGHSYVVYGPLANGATTVMFEGVPSYPDTGRFWEAVDKHQVTIFYTAPTAIRALMREGDAPVKRSSRKSIR 381 ************************************************************************* PP TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437 +lg+vGepinpeaweWy++vvG+e+cpivdtwWqtetGgili+plpg a+++kpgsatlP+fG+++++vd eg NCBI__GCF_000747155.1:WP_034212718.1 382 LLGTVGEPINPEAWEWYHRVVGDERCPIVDTWWQTETGGILISPLPG-AVATKPGSATLPFFGVQPALVDAEG 453 ***********************************************.6************************ PP TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 k++e +e g Lv+ ++wP+++rt+ygd++rf++tYfk+++g+yftGDg+rrd+dGy+wi+GRvDdvinvsGh NCBI__GCF_000747155.1:WP_034212718.1 454 KRLEGATE-GNLVLLDSWPGQMRTVYGDHQRFIDTYFKTYPGTYFTGDGCRRDADGYYWITGRVDDVINVSGH 525 ****8777.79************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 r+gtae+esalv h+avaeaavvg+p++ikg+ i+a+v+lk+g+e++e +l+kel ++vrk igpia+pd ++ NCBI__GCF_000747155.1:WP_034212718.1 526 RMGTAEVESALVGHPAVAEAAVVGAPHDIKGQGIYAYVTLKAGIEPTE-ALRKELVAHVRKDIGPIAAPDWLQ 597 ***********************************************9.5*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaeg......eellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkiae + lgd+stl+dp vv++l + NCBI__GCF_000747155.1:WP_034212718.1 598 WAPGLPKTRSGKIMRRILRKIAEAgpdgvdRAGLGDTSTLADPGVVDSLVN 648 **********************9622222135689************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (653 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: 22.83 // [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