Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011841528.1 RSPH17029_RS11250 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_000015985.1:WP_011841528.1 Length = 653 Score = 839 bits (2167), Expect = 0.0 Identities = 400/626 (63%), Positives = 488/626 (77%), Gaps = 5/626 (0%) Query: 24 YETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLD 83 YE Y S+ DP+ FWGEQGK LDWI PY KVKNT+F PG VSIKW+EDGTLN+A NC+D Sbjct: 27 YERMYAASVADPEAFWGEQGKRLDWIKPYTKVKNTNFRPGEVSIKWFEDGTLNIAWNCID 86 Query: 84 RHLQENGDRTAIIWEGDD-TSQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIYMPMV 142 RHL +TAIIWE DD + ++HISY+ELH +VCR AN L+ G++KGD V +Y+PM+ Sbjct: 87 RHLATRAKQTAIIWEPDDPNAPAQHISYQELHDNVCRMANVLVSQGVRKGDRVVMYLPMI 146 Query: 143 PEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPLKKNV 202 PEAA AMLACARIGA+HSV+F GFSP+A+A RI D +++VITAD R GR PLK N Sbjct: 147 PEAAYAMLACARIGAIHSVVFAGFSPDALANRINDCQAKVVITADTAPRGGRRTPLKSNT 206 Query: 203 DDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPEHQPEAMNAEDPLFIL 262 D AL + + +V+K TG I W +GRD+ ++L+ ASP+ E +NAEDPLFIL Sbjct: 207 DAALLH--CSDRVRCLVVKHTGDQIHWMDGRDVDVKELMRHASPDCPIEEVNAEDPLFIL 264 Query: 263 YTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLA 322 YTSGSTGKPKGV+HT+GGYL YAA T + FDYH GD++WCTADVGWVTGHSY++YGPLA Sbjct: 265 YTSGSTGKPKGVVHTSGGYLTYAAMTHQMTFDYHDGDVFWCTADVGWVTGHSYIVYGPLA 324 Query: 323 CGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRI 382 GATTLMFEGVP +P R V +KH+VN YTAPTAIR+LM G + ++ D SSL++ Sbjct: 325 NGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRSLMGLGPEWVDKYDLSSLKL 384 Query: 383 LGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGSATRPFF 442 LGSVGEPINPEAW WY +GK +CP+VDT+WQTETGG MITPLPGAI +K G+A++PFF Sbjct: 385 LGSVGEPINPEAWSWYNTHVGKGRCPIVDTFWQTETGGHMITPLPGAIPVKPGAASKPFF 444 Query: 443 GVQPALVD-NEGHP-QEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGD 500 GV+P ++D +GH E ATEG L I DSWPGQ RTL+GDHERFE+ YFS +K YF+GD Sbjct: 445 GVKPVILDPTDGHELHETATEGVLCIADSWPGQMRTLWGDHERFEEAYFSQYKGYYFTGD 504 Query: 501 GARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKGQAIY 560 G RRD DGYYW+TGRVDDV+NVSGHR+GTAE+ESALVAH ++AEAAVVG PH IKGQ IY Sbjct: 505 GCRRDADGYYWVTGRVDDVINVSGHRMGTAEVESALVAHAQVAEAAVVGYPHDIKGQGIY 564 Query: 561 AYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAA 620 AYVTL +G +P+ EL ++ WVR EIGP+A+PDV+ W LPKTRSGKIMRRILRKIA Sbjct: 565 AYVTLMNGVQPTEELRKDLVKWVRTEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAE 624 Query: 621 GDTSNLGDTSTLADPGVVEKLLEEKQ 646 D +LGDT+TLADP VV+ L+ ++ Sbjct: 625 NDFGSLGDTTTLADPSVVDDLIANRK 650 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: 1501 Number of extensions: 65 Number of successful extensions: 4 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: 653 Length adjustment: 38 Effective length of query: 614 Effective length of database: 615 Effective search space: 377610 Effective search space used: 377610 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_011841528.1 RSPH17029_RS11250 (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.233840.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 1026.1 0.0 0 1025.9 0.0 1.0 1 NCBI__GCF_000015985.1:WP_011841528.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015985.1:WP_011841528.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1025.9 0.0 0 0 4 628 .. 24 647 .. 21 648 .. 0.99 Alignments for each domain: == domain 1 score: 1025.9 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 + y+++y+ +++dpe+fw++++k +l+w+kp++kv++++++p ++kWfedg+ln+++nc+drh+++r+++ NCBI__GCF_000015985.1:WP_011841528.1 24 AAGYERMYAASVADPEAFWGEQGK-RLDWIKPYTKVKNTNFRPgevSIKWFEDGTLNIAWNCIDRHLATRAKQ 95 5679********************.5***************999889************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aiiwe d+++ +++++Y+el+++vcr+anvl ++Gv+kgdrv++Ylpmipea++amlacaRiGa+hsvvfa NCBI__GCF_000015985.1:WP_011841528.1 96 TAIIWEPDDPNAPAQHISYQELHDNVCRMANVLVSQGVRKGDRVVMYLPMIPEAAYAMLACARIGAIHSVVFA 168 ************************************************************************* PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219 Gfs++ala+Ri+d++ak+vitad++ Rgg++++lk+++d+al +++++v+ +lvvk+tg++++ w +grDv + NCBI__GCF_000015985.1:WP_011841528.1 169 GFSPDALANRINDCQAKVVITADTAPRGGRRTPLKSNTDAALLHCSDRVR-CLVVKHTGDQIH-WMDGRDVDV 239 **********************************************9887.9*********76.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 +el+++ as +c+ e++++edplfiLYtsGstGkPkGv+ht+gGyl++aa+t++++fd++d+d+fwCtaDvGW NCBI__GCF_000015985.1:WP_011841528.1 240 KELMRH-ASPDCPIEEVNAEDPLFILYTSGSTGKPKGVVHTSGGYLTYAAMTHQMTFDYHDGDVFWCTADVGW 311 *****6.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 vtGhsYivygPLanGattl+fegvptypda+rfw+v+ek+kv++fYtaPtaiR+lm lg e+v+k+dlssl++ NCBI__GCF_000015985.1:WP_011841528.1 312 VTGHSYIVYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRSLMGLGPEWVDKYDLSSLKL 384 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eeg 437 lgsvGepinpeaw+Wy+++vGk++cpivdt+WqtetGg++itplpg a+++kpg+a++P+fG++++++d ++g NCBI__GCF_000015985.1:WP_011841528.1 385 LGSVGEPINPEAWSWYNTHVGKGRCPIVDTFWQTETGGHMITPLPG-AIPVKPGAASKPFFGVKPVILDpTDG 456 **********************************************.6*********************999* PP TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 +e++e++++gvL+i ++wP+++rt++gd+erf e+Yf+++kg+yftGDg+rrd+dGy+w++GRvDdvinvsGh NCBI__GCF_000015985.1:WP_011841528.1 457 HELHETATEGVLCIADSWPGQMRTLWGDHERFEEAYFSQYKGYYFTGDGCRRDADGYYWVTGRVDDVINVSGH 529 ****99999**************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 r+gtae+esalv+h +vaeaavvg+p++ikg+ i+a+v+l++gv+++ee l+k+l k+vr+eigpia+pd i+ NCBI__GCF_000015985.1:WP_011841528.1 530 RMGTAEVESALVAHAQVAEAAVVGYPHDIKGQGIYAYVTLMNGVQPTEE-LRKDLVKWVRTEIGPIASPDVIQ 601 ***********************************************95.*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkiae++ +lgd++tl+dpsvv++l++ NCBI__GCF_000015985.1:WP_011841528.1 602 WAPGLPKTRSGKIMRRILRKIAENDfGSLGDTTTLADPSVVDDLIA 647 ******************************************9975 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: 30.53 // [ok]
This GapMind analysis is from Apr 10 2024. 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