Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate H281DRAFT_02796 H281DRAFT_02796 acetate kinase
Query= SwissProt::P74879 (404 letters) >FitnessBrowser__Burk376:H281DRAFT_02796 Length = 385 Score = 242 bits (618), Expect = 1e-68 Identities = 157/389 (40%), Positives = 207/389 (53%), Gaps = 28/389 (7%) Query: 3 YKIMAINAGSSSLKFQLLEMPQGD--MLCQGLIERIGMADAQVTIKTHSQKW--QETVPV 58 + I+ +N+GSSSLKF L E D +L +G + IG D ++ I + QE + Sbjct: 10 HTILVLNSGSSSLKFGLFEHSGDDESLLLEGSAQGIGRRDGRLRIAAPDGRVLVQEEHVL 69 Query: 59 ADHRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAEL 118 DA L+KL VGHRV HGG + +T E +++ Sbjct: 70 ESQTDA----LQKLSTVLAQQHHEQPTAVGHRVVHGGPHLRSHQRLTPEVRRRLQDAVHF 125 Query: 119 APLHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGF 178 APLH P I +++ A A FDTAFH TL A LP Y+E G+ RYGF Sbjct: 126 APLHIPPALDLIDEAQKIFGGAQHFACFDTAFHATLPPRAAQLALP-RRYSEAGVIRYGF 184 Query: 179 HGTSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMG 238 HG S++ L +LG L A RV+C HLGNGSS+CA+++GRSV+TSMG TP GV MG Sbjct: 185 HGLSYES----LVAQLGATLPA-RVVCAHLGNGSSVCALRDGRSVDTSMGMTPTGGVPMG 239 Query: 239 TRSGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAK 298 TR GD+DP +L ++ + E L LLN SGL G + SD + +EQ A G+ A Sbjct: 240 TRCGDLDPGVLLYLMRVEKLDANGLETLLNRHSGLAGYADGESDMQALEQRAAAGDPHAS 299 Query: 299 LALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKN 358 LAL FA +R TIG Y +GG+D LVFTGGIGE+S + R +C L FLGL Sbjct: 300 LALDAFATAVRKTIGGYAALLGGIDLLVFTGGIGEHSVQMRKRICEGLSFLGL------- 352 Query: 359 QRNATFIQTENALVKVAVINTNEELMIAQ 387 +A KV V++T EE IA+ Sbjct: 353 -------HEGDASGKVRVLHTEEEKQIAR 374 Lambda K H 0.319 0.135 0.392 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: 363 Number of extensions: 15 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: 404 Length of database: 385 Length adjustment: 31 Effective length of query: 373 Effective length of database: 354 Effective search space: 132042 Effective search space used: 132042 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate H281DRAFT_02796 H281DRAFT_02796 (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.31806.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-96 308.5 0.0 8.3e-96 307.1 0.0 1.6 1 lcl|FitnessBrowser__Burk376:H281DRAFT_02796 H281DRAFT_02796 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_02796 H281DRAFT_02796 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.1 0.0 8.3e-96 8.3e-96 4 360 .. 10 354 .. 7 381 .. 0.92 Alignments for each domain: == domain 1 score: 307.1 bits; conditional E-value: 8.3e-96 TIGR00016 4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktv.edgekkeeeklaiedheea 67 + ilvln+Gssslkf l+++++ e++ll+g ++ i + r+ + dg +e+ e+++ a lcl|FitnessBrowser__Burk376:H281DRAFT_02796 10 HTILVLNSGSSSLKFGLFEHSGdDESLLLEGSAQGIGRRDGRLRIAaPDGRVLVQEEHVLESQTDA 75 689****************997467779*********999988877356666778888899999** PP TIGR00016 68 vkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaeleg 133 ++kl + l + +++++ +++GHRvvhGg ++ + +t ev ++++d++++APlH p++l+ lcl|FitnessBrowser__Burk376:H281DRAFT_02796 76 LQKLSTVLAQ-----QHHEQPTAVGHRVVHGGPHLRSHQRLTPEVRRRLQDAVHFAPLHIPPALDL 136 ***9999995.....778999********************************************* PP TIGR00016 134 ieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakl 199 i++++ k+ a++ a+FDtafH t+p +a+ alP + y e gv rYGfHG+s++ + ++ + lcl|FitnessBrowser__Burk376:H281DRAFT_02796 137 IDEAQ--KIFGGAQHFACFDTAFHATLPPRAAQLALP-RRYSEAGVIRYGFHGLSYESLVAQLGAT 199 *****..7778888***********************.678999************9777776666 PP TIGR00016 200 lnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls 265 l +++ +HlGnG+sv+a+++G+s+dtsmG+tP G+ mGtR+Gd+Dp+++ yl+ ++l lcl|FitnessBrowser__Burk376:H281DRAFT_02796 200 LPA-----RVVCAHLGNGSSVCALRDGRSVDTSMGMTPTGGVPMGTRCGDLDPGVLLYLMRVEKLD 260 655.....89******************************************************** PP TIGR00016 266 ldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDa 331 ++ +e++ln++sGl g ++ sD+ ++++ ++g+ +a+lAl+ ++ ++k ig y+a l g +D lcl|FitnessBrowser__Burk376:H281DRAFT_02796 261 ANGLETLLNRHSGLAGYADGESDMQALEQRAAAGDPHASLALDAFATAVRKTIGGYAALLGG-IDL 325 ************************************************************66.*** PP TIGR00016 332 ivFtgGiGenaaevrelvleklevlGlkl 360 +vFtgGiGe ++++r++++e+l +lGl+ lcl|FitnessBrowser__Burk376:H281DRAFT_02796 326 LVFTGGIGEHSVQMRKRICEGLSFLGLHE 354 **************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (385 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 3.45 // [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