Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate AZOBR_RS12495 AZOBR_RS12495 acetate kinase
Query= SwissProt::P37877 (395 letters) >FitnessBrowser__azobra:AZOBR_RS12495 Length = 402 Score = 284 bits (726), Expect = 4e-81 Identities = 168/390 (43%), Positives = 234/390 (60%), Gaps = 15/390 (3%) Query: 4 IIAINAGSSSLKFQLFEMPSETVLTKGLVERI-GIADSVFTISVNGEKNTEVTDI----- 57 I+ INAGSSSLKF +F L + +I GI + + KN + Sbjct: 12 ILVINAGSSSLKFSVFRESGAGGLRVTINGQISGIGTEPKFEAKDAAKNPLAERVWAAGE 71 Query: 58 PDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISEL 117 P A+ L + E + D ++ GHRVVHGG + + VLLT ++E+E L Sbjct: 72 PSDRTALLAFLLEWIEGRL--DGAKLLAAGHRVVHGGTRHAAPVLLTPAVMEELESFIPL 129 Query: 118 APLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGF 177 APLH P N+ I+A E P +P VA FDTAFH+ P QS ++++P E ++ G+R+YGF Sbjct: 130 APLHQPHNLAAIRALAEAHPELPQVACFDTAFHRGQPWQSQMFAIPRELTDE-GVRRYGF 188 Query: 178 HGTSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMG 237 HG S++Y+ R EL L D R++ HLG+GAS+ A+ G+S+D++MGFT L G+ MG Sbjct: 189 HGLSYEYIARRLPELAPE-LADGRVVVAHLGSGASMCAIHAGRSVDSTMGFTALDGLPMG 247 Query: 238 TRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAE 297 TR GNIDP ++ Y+M + G AD + L KSGLLG+SG S+D+R ++++ + AE Sbjct: 248 TRCGNIDPGVLIYLMRQKGMGADAIEKLLYNKSGLLGVSGLSNDMRALLDSE---DPHAE 304 Query: 298 TALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALN 357 A+E+F RI K G+ AA M G+DA++FTAGIGE S VR RV L ++GV DPA N Sbjct: 305 EAVELFCFRIAKETGALAASMGGIDALVFTAGIGERSAPVRARVGDKLAWLGVILDPAAN 364 Query: 358 NVRGEEAFISYPHSPVKVMIIPTDEEVMIA 387 G IS P+S + V +IPTDEE MIA Sbjct: 365 EANG--PLISAPNSRIPVYVIPTDEEQMIA 392 Lambda K H 0.317 0.136 0.381 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: 378 Number of extensions: 28 Number of successful extensions: 6 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: 395 Length of database: 402 Length adjustment: 31 Effective length of query: 364 Effective length of database: 371 Effective search space: 135044 Effective search space used: 135044 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 AZOBR_RS12495 AZOBR_RS12495 (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.19533.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-114 369.0 0.0 1.5e-114 368.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS12495 AZOBR_RS12495 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS12495 AZOBR_RS12495 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.8 0.0 1.5e-114 1.5e-114 5 399 .. 11 394 .. 8 400 .. 0.90 Alignments for each domain: == domain 1 score: 368.8 bits; conditional E-value: 1.5e-114 TIGR00016 5 kilvlnaGssslkfalldaen..sekvllsglverikleeariktv.edge..kkeeeklaiedheeav 68 ilv+naGssslkf+++ ++ + +v ++g + i e ++ + ++ ++ + + +d+++ + lcl|FitnessBrowser__azobra:AZOBR_RS12495 11 AILVINAGSSSLKFSVFRESGagGLRVTINGQISGIGTEPKFEAKDaAKNPlaERVWAAGEPSDRTALL 79 79***************9998545677899999999988664443313443112333445556677777 PP TIGR00016 69 kkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieav 137 ++ll+ ++ + + +++ + GHRvvhGg++++ v++t v+++++ +++lAPlH p +l +i+a+ lcl|FitnessBrowser__azobra:AZOBR_RS12495 80 AFLLEWIEG----RLDGAKLLAAGHRVVHGGTRHAAPVLLTPAVMEELESFIPLAPLHQPHNLAAIRAL 144 777777775....5678899999********************************************** PP TIGR00016 138 lklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206 + +++ ++va+FDtafH+ p ++ ++a+P++l ++ gvRrYGfHG+s++y+++r+ +l l+d lcl|FitnessBrowser__azobra:AZOBR_RS12495 145 A--EAHPELPQVACFDTAFHRGQPWQSQMFAIPREL-TDEGVRRYGFHGLSYEYIARRLPELAPE-LAD 209 9..99999*************************776.567*******************997665.9** PP TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnk 275 +++v+HlG Gas++a++ G+s+d +mG+t L+Gl mGtR+G+iDp+++ yl+ ++g+ +d+ie++l lcl|FitnessBrowser__azobra:AZOBR_RS12495 210 GRVVVAHLGSGASMCAIHAGRSVDSTMGFTALDGLPMGTRCGNIDPGVLIYLMRQKGMGADAIEKLLYN 278 ********************************************************************* PP TIGR00016 276 ksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaae 344 ksGllg+sgls+D+R +ld + +a+ A+++++ Riak g+ +as+ g +Da+vFt+GiGe +a lcl|FitnessBrowser__azobra:AZOBR_RS12495 279 KSGLLGVSGLSNDMRALLDSE---DPHAEEAVELFCFRIAKETGALAASMGG-IDALVFTAGIGERSAP 343 ******************998...6679**********************76.**************** PP TIGR00016 345 vrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeD 399 vr++v +kl+ lG+ ld++ n+ + +is ++s++ v+vipt+ee +ia lcl|FitnessBrowser__azobra:AZOBR_RS12495 344 VRARVGDKLAWLGVILDPAANE----ANGPLISAPNSRIPVYVIPTDEEQMIALH 394 *******************999....7789**********************976 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: 12.05 // [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