Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 208544 DVU3030 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >MicrobesOnline__882:208544 Length = 402 Score = 433 bits (1114), Expect = e-126 Identities = 222/404 (54%), Positives = 285/404 (70%), Gaps = 8/404 (1%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-----GDEKHVIERE 55 M VLVINSGSSSIKYQLI+ME E LC G+ ERIG +L H++ G+EK E+ Sbjct: 1 MNVLVINSGSSSIKYQLIDMEREVPLCSGLVERIGEPMGKLTHKIRPDAEGEEKLTFEQP 60 Query: 56 LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115 +H E +K ++ + D GVIKD EI A+GHRV+ GGE K+SV +D+ I + Sbjct: 61 FTNHVEGMKRVVELITDADKGVIKDKSEIGAIGHRVLLGGEEIKQSVRIDDWAKGVIRDY 120 Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175 PL PLHNPANL GI+ A +L PG+PNV VFDT FHQ++P KAYLY +P E YE+ KIRR Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPGLPNVGVFDTEFHQSMPAKAYLYPLPIELYEELKIRR 180 Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235 YGFHGTSHRY++KR A+ LGK L+EL IITCH+GNG S+AAVK GKCVDT+MG TPLEGL Sbjct: 181 YGFHGTSHRYITKRTAQYLGKPLDELNIITCHLGNGCSMAAVKNGKCVDTTMGITPLEGL 240 Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295 +MGTR GD+DPAI F+MEK+ +SP E ++NK+SG+ G+ +DMRD+ A G+ Sbjct: 241 MMGTRCGDIDPAIVPFLMEKKNLSPAEADTLMNKQSGLKGMCG--MNDMRDLHAARENGN 298 Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355 E +L E++ YRI KYIGAY A + VDA+VFTAG+GEN R +VC+ L+ LG+ +D Sbjct: 299 ERAQLAFEMFTYRIKKYIGAYYAVLGRVDAVVFTAGIGENDDFVRAEVCAGLDSLGIAVD 358 Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVE 399 +N G+ IS SRV VLVVPTNEEL IA+ T ++++ Sbjct: 359 PARN-AVRNGQPRHISPDGSRVAVLVVPTNEELEIAQATLDVLK 401 Lambda K H 0.318 0.138 0.391 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: 484 Number of extensions: 23 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: 403 Length of database: 402 Length adjustment: 31 Effective length of query: 372 Effective length of database: 371 Effective search space: 138012 Effective search space used: 138012 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate 208544 DVU3030 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))
# 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/TIGR00016.hmm # target sequence database: /tmp/gapView.29743.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00016 [M=405] Accession: TIGR00016 Description: ackA: acetate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-150 485.1 0.0 7.9e-150 485.0 0.0 1.0 1 lcl|MicrobesOnline__882:208544 DVU3030 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208544 DVU3030 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.0 0.0 7.9e-150 7.9e-150 5 402 .. 2 398 .. 1 401 [. 0.95 Alignments for each domain: == domain 1 score: 485.0 bits; conditional E-value: 7.9e-150 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikleeariktv....edgekkeeeklaiedheeavkkllntlkk.d 78 +lv+n+Gsss+k++l+d+e e l+sglveri + +++ + +ge+k ++++ +++h e++k++++ +++ d lcl|MicrobesOnline__882:208544 2 NVLVINSGSSSIKYQLIDME-REVPLCSGLVERIGEPMGKLTHKirpdAEGEEKLTFEQPFTNHVEGMKRVVELITDaD 79 79******************.5888*********98765544432343678888999999****************999 PP TIGR00016 79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafH 157 k ++k++sei +iGHRv Gge+ ++sv ++d + i+d ++l PlHnpa+l gie + +l+ + +nv vFDt fH lcl|MicrobesOnline__882:208544 80 KGVIKDKSEIGAIGHRVLLGGEEIKQSVRIDDWAKGVIRDYIPLGPLHNPANLAGIEVAEELF--PGLPNVGVFDTEFH 156 ************************************************************555..5567********** PP TIGR00016 158 qtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGlt 236 q +p +aylY+lP +ly+el++RrYGfHGtsh+y+t+r+a++l+kpld+ln+i+cHlGnG s++avknGk++dt+mG+t lcl|MicrobesOnline__882:208544 157 QSMPAKAYLYPLPIELYEELKIRRYGFHGTSHRYITKRTAQYLGKPLDELNIITCHLGNGCSMAAVKNGKCVDTTMGIT 235 ******************************************************************************* PP TIGR00016 237 PLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRia 315 PLeGl+mGtR+GdiDpai+ +l+e+++ls +e +++nk+sGl g+ g +D+Rd+ ++ e+gne+a+lA++++++Ri+ lcl|MicrobesOnline__882:208544 236 PLEGLMMGTRCGDIDPAIVPFLMEKKNLSPAEADTLMNKQSGLKGMCG-MNDMRDLHAARENGNERAQLAFEMFTYRIK 313 ************************************************.89**************************** PP TIGR00016 316 kyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneel 394 kyig+y a l g++Da+vFt+GiGen+ vr++v+ +l++lG+++d+++n r+g+ + is + s+v vlv+ptneel lcl|MicrobesOnline__882:208544 314 KYIGAYYAVL-GRVDAVVFTAGIGENDDFVRAEVCAGLDSLGIAVDPARNA-VRNGQPRHISPDGSRVAVLVVPTNEEL 390 **********.67*************************************9.999************************ PP TIGR00016 395 viaeDalr 402 ia+ +l lcl|MicrobesOnline__882:208544 391 EIAQATLD 398 ***98776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (402 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: 11.76 // [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