Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate 3608653 Dshi_5006 hypothetical protein (NCBI)
Query= curated2:Q6N143 (398 letters) >FitnessBrowser__Dino:3608653 Length = 385 Score = 283 bits (723), Expect = 8e-81 Identities = 172/394 (43%), Positives = 230/394 (58%), Gaps = 20/394 (5%) Query: 2 SDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDGSTRYDTYL 61 SD++LVLNAGSSS+KFAL+ T A+HL G S+G K+ G+ L Sbjct: 7 SDLILVLNAGSSSLKFALF---TPALAEHLT--GQAESIGGPGRLKI----GARSASCDL 57 Query: 62 PEGTSHDDAMAVLIGWIETT-FPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDR 120 P+ H A+A ++ + T L AV HRVVHGG PV +TP +++ A Sbjct: 58 PD---HGAALAAILEALATRGITASHLKAVAHRVVHGGVRLTAPVRITPATRSEIAACSA 114 Query: 121 LAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGF 180 LAPLH PHN++AI+ + L P +PQ A FDTAFH PEVA + LP G+RRYGF Sbjct: 115 LAPLHNPHNLAAIDRITALMPDVPQCASFDTAFHASNPEVALRYGLPDTAETAGLRRYGF 174 Query: 181 HGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMG 240 HG SY + V G A+ D R++ HLG+GAS+CA+ RS+ATTMG++ L+GL M Sbjct: 175 HGQSYAAMVDSWSRVTGAALPD-RLLAFHLGSGASICAIRDGRSVATTMGYSPLEGLTMA 233 Query: 241 SRCGELDPGVVLYLLEEKSMT-AREIEDLLYRESGLLGVSGISDDMRTLLASDDPHACEA 299 +R G +D VL L E+ + AR I L ESGL G+SG DMRTL+ASD P A A Sbjct: 234 TRSGSIDGNAVLKLAEDHGIARARRI---LNNESGLAGLSGGLSDMRTLMASDRPEAGFA 290 Query: 300 IELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDANAS 359 ++ FVY R SL A LGG + + FTGGIGE+A+EIR R+ W+G +DP+ANA Sbjct: 291 VDHFVYWAVRHASSLLAPLGGTETIAFTGGIGENAAEIRARIVAGLHWIGAEIDPEANA- 349 Query: 360 LSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393 G + + S + IP +E+ M+A R+ Sbjct: 350 -EGQTALHSAASATGIYIIPAEEERMLAADALRV 382 Lambda K H 0.321 0.137 0.413 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: 478 Number of extensions: 26 Number of successful extensions: 5 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: 398 Length of database: 385 Length adjustment: 31 Effective length of query: 367 Effective length of database: 354 Effective search space: 129918 Effective search space used: 129918 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate 3608653 Dshi_5006 (hypothetical protein (NCBI))
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.19682.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-94 301.3 0.0 5.4e-94 301.1 0.0 1.0 1 lcl|FitnessBrowser__Dino:3608653 Dshi_5006 hypothetical protein ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608653 Dshi_5006 hypothetical protein (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 301.1 0.0 5.4e-94 5.4e-94 3 403 .. 7 382 .. 5 384 .. 0.93 Alignments for each domain: == domain 1 score: 301.1 bits; conditional E-value: 5.4e-94 TIGR00016 3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdk 79 s +ilvlnaGssslkfal+ + +e++ g +e i ++ + + g +++ + +dh +a++++l++l + + lcl|FitnessBrowser__Dino:3608653 7 SDLILVLNAGSSSLKFALFTPALAEHL--TGQAESIGGPGR-L---KIG--ARSASCDLPDHGAALAAILEALAT-R 74 678*******************77766..9*******9999.3...334..4568899****************6.6 PP TIGR00016 80 kilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtaf 156 i + s+++++ HRvvhGg ++t v +t + ++i+ s lAPlHnp +l +i+ ++ ++++++ a FDtaf lcl|FitnessBrowser__Dino:3608653 75 GI--TASHLKAVAHRVVHGGVRLTAPVRITPATRSEIAACSALAPLHNPHNLAAIDRIT--ALMPDVPQCASFDTAF 147 66..5689***************************************************..889999********** PP TIGR00016 157 HqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsm 233 H pe a Y+lP + + g+RrYGfHG s+ + ++ +++ + +l d +l+ HlG Gas++a+++G+s+ t+m lcl|FitnessBrowser__Dino:3608653 148 HASNPEVALRYGLP-DTAETAGLRRYGFHGQSYAAMVDSWSRVTGAALPD-RLLAFHLGSGASICAIRDGRSVATTM 222 **************.788899*********************99997765.899*********************** PP TIGR00016 234 GltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvy 310 G PLeGl m tRsG+iD ++ lae +g + ++ln +sGl g+sg sD+R++++ + ea A++ + lcl|FitnessBrowser__Dino:3608653 223 GYSPLEGLTMATRSGSIDGNAVLKLAEDHGIA--RARRILNNESGLAGLSGGLSDMRTLMASD---RPEAGFAVDHF 294 **********************9999988765..668**********************9877...7789******* PP TIGR00016 311 vhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlv 387 v+ ++ ++ +a l g ++i FtgGiGenaae+r++++ +l+ +G ++d+e n + ++ + + s++ +++ lcl|FitnessBrowser__Dino:3608653 295 VYWAVRHASSLLAPLGG-TETIAFTGGIGENAAEIRARIVAGLHWIGAEIDPEANA----EGQTALHSAASATGIYI 366 ***************77.9***********************************99....55666777999****** PP TIGR00016 388 iptneelviaeDalrl 403 ip +ee ++a Dalr+ lcl|FitnessBrowser__Dino:3608653 367 IPAEEERMLAADALRV 382 *************997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.94 // [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