Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_097068839.1 CRO22_RS01345 acetate--CoA ligase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >NCBI__GCF_900217815.1:WP_097068839.1 Length = 644 Score = 828 bits (2140), Expect = 0.0 Identities = 409/631 (64%), Positives = 477/631 (75%), Gaps = 5/631 (0%) Query: 16 NTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTL 75 N + Y MY++S+ NPD FW + KRLDW+ P+T VK T F V IKWF DG L Sbjct: 10 NAHANNQKYLEMYRESIENPDAFWGREGKRLDWMTPYTKVKNTDFTFGKVSIKWFEDGVL 69 Query: 76 NVSYNCLDRHLAERGDQIAIIWEGDDPAE-SRNITYRELHEQVCKFANALRGQDVHRGDV 134 N S NC+DRHL +R Q AII+E DDP+E +++ITY+EL E+V + AN L Q + RGD Sbjct: 70 NASVNCIDRHLRDRALQTAIIFEPDDPSEPAQHITYKELSEKVNRMANVLLSQGIMRGDR 129 Query: 135 VTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGLRAGK 194 V IY+PMIPEA AMLAC RIGAIHS+VF GFSP+ALA RI DC +K+VITAD R G+ Sbjct: 130 VVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALANRINDCGAKLVITADTAPRGGR 189 Query: 195 KISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGTVCAPKEMG 254 + LKAN D AL + S + +V KRTG I W RD+ LM+ C P+ M Sbjct: 190 RTPLKANTDAALLH--CSDKVRCLVVKRTGDQISWVHGRDVDLLYLMEHVSPECPPRPMN 247 Query: 255 AEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTADVGWVTGHT 314 AE+ LFILYTSGSTGKPKGV HTTGGYL YAA+TH+ FDY+ G+++WCTADVGWVTGH+ Sbjct: 248 AEDPLFILYTSGSTGKPKGVVHTTGGYLCYAAMTHQYTFDYQDGDVFWCTADVGWVTGHS 307 Query: 315 YIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMAQGTAAVEG 374 YI+YGPLANGATTL+FEGVP YPD R + +KHKVN YTAPTAIRA+M QGT VE Sbjct: 308 YIIYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEK 367 Query: 375 ADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPLPGAHGLKP 434 D SSL++LGSVGEPINPEAW WY K++G+ +CPIVDT+WQTETG +++PLPGA KP Sbjct: 368 YDLSSLKVLGSVGEPINPEAWVWYDKHIGKGKCPIVDTFWQTETGGHMITPLPGATPTKP 427 Query: 435 GSAARPFFGVVPALVD--NLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTF 492 GSA PFFGV P ++D I E EG L I DSWPGQ RT++GDHDRF +TYF + Sbjct: 428 GSATNPFFGVKPVVLDPQTAVRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQY 487 Query: 493 RGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPH 552 RG YFTGDG RRD DGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAH +VAEAAVVG PH Sbjct: 488 RGYYFTGDGCRRDKDGYYWITGRVDDVINVSGHRMGTAEVESALVAHQQVAEAAVVGYPH 547 Query: 553 DIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 612 DIKGQGIY YVTL G EPSE LR +L WVR EIGPIASPD+IQWAPGLPKTRSGKIMR Sbjct: 548 DIKGQGIYAYVTLMNGVEPSEELRKDLVKWVRTEIGPIASPDLIQWAPGLPKTRSGKIMR 607 Query: 613 RILRKIATGEYDGLGDISTLADPGVVQHLID 643 RILRKIA +Y LGDISTLADP VVQ LID Sbjct: 608 RILRKIAENDYGALGDISTLADPSVVQELID 638 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: 1430 Number of extensions: 59 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: 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 WP_097068839.1 CRO22_RS01345 (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.3010808.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 1027.2 0.0 0 1027.0 0.0 1.0 1 NCBI__GCF_900217815.1:WP_097068839.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900217815.1:WP_097068839.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1027.0 0.0 0 0 3 628 .. 14 638 .. 12 639 .. 0.98 Alignments for each domain: == domain 1 score: 1027.0 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 ++++y e+y+e+ie+p++fw++++k +l+w++p++kv++++++ ++kWfedg ln+s+nc+drh+++r+ NCBI__GCF_900217815.1:WP_097068839.1 14 NNQKYLEMYRESIENPDAFWGREGK-RLDWMTPYTKVKNTDFTFgkvSIKWFEDGVLNASVNCIDRHLRDRAL 85 7899*********************.5**************9877789************************* PP TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145 ++aii+e d+++e ++++tY+el ++v+r+anvl ++G+ +gdrv+iYlpmipea++amlacaRiGa+hs+vf NCBI__GCF_900217815.1:WP_097068839.1 86 QTAIIFEPDDPSEPAQHITYKELSEKVNRMANVLLSQGIMRGDRVVIYLPMIPEAAYAMLACARIGAIHSIVF 158 ************************************************************************* PP TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvw 218 aGfs++ala+Ri+d+ aklvitad++ Rgg++++lk+++d+al +++++v+ +lvvkrtg++++ w++grDv NCBI__GCF_900217815.1:WP_097068839.1 159 AGFSPDALANRINDCGAKLVITADTAPRGGRRTPLKANTDAALLHCSDKVR-CLVVKRTGDQIS-WVHGRDVD 229 ***********************************************9997.9*********76.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 + l+e+ +s ec+p+++++edplfiLYtsGstGkPkGv+httgGyl +aa+t++y+fd++d+d+fwCtaDvG NCBI__GCF_900217815.1:WP_097068839.1 230 LLYLMEH-VSPECPPRPMNAEDPLFILYTSGSTGKPKGVVHTTGGYLCYAAMTHQYTFDYQDGDVFWCTADVG 301 ******6.***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364 WvtGhsYi+ygPLanGattl+fegvptypda+rfw+v+ek+kv++fYtaPtaiRalm +g+e+v+k+dlssl+ NCBI__GCF_900217815.1:WP_097068839.1 302 WVTGHSYIIYGPLANGATTLMFEGVPTYPDAGRFWAVCEKHKVNQFYTAPTAIRALMGQGTEWVEKYDLSSLK 374 ************************************************************************* PP TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.ee 436 vlgsvGepinpeaw Wy +++Gk+kcpivdt+WqtetGg++itplpg at++kpgsat+P+fG++++v+d ++ NCBI__GCF_900217815.1:WP_097068839.1 375 VLGSVGEPINPEAWVWYDKHIGKGKCPIVDTFWQTETGGHMITPLPG-ATPTKPGSATNPFFGVKPVVLDpQT 446 ***********************************************.6*********************666 PP TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509 + ++ e e +gvL+i+++wP+++rt++gd++rf+etYf +++g+yftGDg+rrdkdGy+wi+GRvDdvinvsG NCBI__GCF_900217815.1:WP_097068839.1 447 AVRIGEVECEGVLCISDSWPGQMRTVWGDHDRFQETYFGQYRGYYFTGDGCRRDKDGYYWITGRVDDVINVSG 519 6667799999*************************************************************** PP TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582 hr+gtae+esalv+h++vaeaavvg+p++ikg+ i+a+v+l++gve++ee l+k+l k+vr+eigpia+pd i NCBI__GCF_900217815.1:WP_097068839.1 520 HRMGTAEVESALVAHQQVAEAAVVGYPHDIKGQGIYAYVTLMNGVEPSEE-LRKDLVKWVRTEIGPIASPDLI 591 *************************************************5.********************** PP TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++++ lPktRsGkimRR+lrkiae++ +lgd+stl+dpsvv+el++ NCBI__GCF_900217815.1:WP_097068839.1 592 QWAPGLPKTRSGKIMRRILRKIAENDyGALGDISTLADPSVVQELID 638 **************************99***************9986 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 18.99 // [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