Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4702 PP_4702 acetyl-CoA synthetase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >FitnessBrowser__Putida:PP_4702 Length = 644 Score = 861 bits (2224), Expect = 0.0 Identities = 408/637 (64%), Positives = 491/637 (77%), Gaps = 4/637 (0%) Query: 7 YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66 YP V+ + Y+ +Y+QSV +PD FW EQAKRLDWIKP+++V+Q D H Sbjct: 7 YPQALAVSQSAALTPEDYRRLYRQSVEDPDTFWAEQAKRLDWIKPWSSVQQC--DLHTGK 64 Query: 67 IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKFANALRG 126 +WF LNVSYNC+DRHLA+RG+Q A++WEGDDP +S+ ITYRELH QVC+ ANA++ Sbjct: 65 ARWFDGAQLNVSYNCIDRHLAQRGEQTALLWEGDDPKDSKAITYRELHRQVCRLANAMKA 124 Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186 + V +GD V+IYMPMIPEA AMLACTRIGAIHSVVFGGFSP+AL RI+D + VITA Sbjct: 125 RGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDALRDRILDADCRTVITA 184 Query: 187 DEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGT 246 DEG+R GK+I LK NVD AL + ++ V+V +RTGG++ W + RD+WY + K AG Sbjct: 185 DEGVRGGKRIPLKQNVDKALAS--CPAVSSVLVVRRTGGDVAWTEGRDLWYHEATKDAGD 242 Query: 247 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTAD 306 C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL A +T + VFDYR GE++WCTAD Sbjct: 243 DCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTAD 302 Query: 307 VGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMA 366 VGWVTGH+YIVYGPLANGA +L+FEGVPNYPD +R +++DKH+VNI YTAPTA+RA+M Sbjct: 303 VGWVTGHSYIVYGPLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMR 362 Query: 367 QGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPL 426 +G+A ++ SLRLLGSVGEPINPEAWEWY++ VGQ RCPIVDTWWQTETG +++PL Sbjct: 363 EGSAPLQSTSRKSLRLLGSVGEPINPEAWEWYFEEVGQKRCPIVDTWWQTETGGIMLTPL 422 Query: 427 PGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVD 486 PG LKPG A +P FGV P L+D G +IEG G L I SWPGQ R++YGDH R VD Sbjct: 423 PGTQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGAGVLAIKASWPGQIRSVYGDHQRMVD 482 Query: 487 TYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 546 TYFK G YFTGDGARRDADG +WITGR+DDV+NVSGHR+GTAE+ESA+V H VAEAA Sbjct: 483 TYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSVAEAA 542 Query: 547 VVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 606 VVG PHD+KGQG+Y +VT G P + L+ EL V KEIG A P++IQWAP LPKTR Sbjct: 543 VVGYPHDLKGQGVYAFVTTMNGVTPDDTLKAELLALVSKEIGSFAKPELIQWAPALPKTR 602 Query: 607 SGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643 SGKIMRRILRKIA E + LGD STLADP VVQ LID Sbjct: 603 SGKIMRRILRKIACNELENLGDTSTLADPSVVQGLID 639 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: 1451 Number of extensions: 70 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: 644 Length adjustment: 38 Effective length of query: 613 Effective length of database: 606 Effective search space: 371478 Effective search space used: 371478 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 PP_4702 PP_4702 (acetyl-CoA synthetase)
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.29937.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 1039.4 0.0 0 1039.2 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4702 PP_4702 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4702 PP_4702 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1039.2 0.0 0 0 4 628 .. 21 639 .. 18 640 .. 0.98 Alignments for each domain: == domain 1 score: 1039.2 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvaii 77 e+y++ly++++edp++fwa++ak+ l+w+kp+++v++++l++ k++Wf++++lnvsync+drh+++r +++a+ lcl|FitnessBrowser__Putida:PP_4702 21 PEDYRRLYRQSVEDPDTFWAEQAKR-LDWIKPWSSVQQCDLHTgKARWFDGAQLNVSYNCIDRHLAQRGEQTALL 94 689*********************5.***************999******************************* PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152 wegd+++ ds+++tY+el+r+vcrlan++k+ Gvkkgdrv+iY+pmipea++amlac+RiGa+hsvvf+Gfs++a lcl|FitnessBrowser__Putida:PP_4702 95 WEGDDPK-DSKAITYRELHRQVCRLANAMKARGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDA 168 ******9.5****************************************************************** PP TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekea 227 l++Ri da++++vitadeg+Rggk+i+lk++vd+al++++ +v++vlvv+rtg +va w+egrD+w++e++++ a lcl|FitnessBrowser__Putida:PP_4702 169 LRDRILDADCRTVITADEGVRGGKRIPLKQNVDKALASCP-AVSSVLVVRRTGGDVA-WTEGRDLWYHEATKD-A 240 ***************************************9.7*************77.**************7.* PP TIGR02188 228 saecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302 ++c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+a++t+k+vfd++d+++fwCtaDvGWvtGhsYivyg lcl|FitnessBrowser__Putida:PP_4702 241 GDDCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTADVGWVTGHSYIVYG 315 *************************************************************************** PP TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpea 377 PLanGa +l+fegvp+ypd+srfw+v++k++v+ifYtaPta+Ralm++g++ +++++++slr+lgsvGepinpea lcl|FitnessBrowser__Putida:PP_4702 316 PLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMREGSAPLQSTSRKSLRLLGSVGEPINPEA 390 *************************************************************************** PP TIGR02188 378 weWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvik 452 weWy+e+vG+++cpivdtwWqtetGgi++tplpg + +lkpg+at+P+fG++++++de+gk +e gvL+ik lcl|FitnessBrowser__Putida:PP_4702 391 WEWYFEEVGQKRCPIVDTWWQTETGGIMLTPLPG-TQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGA-GVLAIK 463 **********************************.6***************************97666.8***** PP TIGR02188 453 kpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheav 527 +wP+++r++ygd++r+v+tYfk l+g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h++v lcl|FitnessBrowser__Putida:PP_4702 464 ASWPGQIRSVYGDHQRMVDTYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSV 538 *************************************************************************** PP TIGR02188 528 aeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllr 602 aeaavvg+p+++kg+ ++afv+ ++gv++d++ l++el +lv+keig++akp+ i+++++lPktRsGkimRR+lr lcl|FitnessBrowser__Putida:PP_4702 539 AEAAVVGYPHDLKGQGVYAFVTTMNGVTPDDT-LKAELLALVSKEIGSFAKPELIQWAPALPKTRSGKIMRRILR 612 *******************************5.****************************************** PP TIGR02188 603 kiaege.ellgdvstledpsvveelke 628 kia +e e+lgd+stl+dpsvv+ l++ lcl|FitnessBrowser__Putida:PP_4702 613 KIACNElENLGDTSTLADPSVVQGLID 639 **********************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (644 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: 00:00:00.04 # Mc/sec: 8.34 // [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