Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate HSERO_RS01305 HSERO_RS01305 acetate kinase
Query= curated2:Q1QPW6 (404 letters) >FitnessBrowser__HerbieS:HSERO_RS01305 Length = 397 Score = 311 bits (798), Expect = 2e-89 Identities = 182/402 (45%), Positives = 247/402 (61%), Gaps = 19/402 (4%) Query: 4 ILVVNAGSSSVKFQVFSAEGEGKLLRQIKGQVDGIGSRP---RLRASGADNEPLADRAYP 60 +L NAGSS++K VF +G + + +GQ+D + P RL G +E Sbjct: 5 LLTFNAGSSTIKLGVFRLDG-ARARKIGQGQLD-LHLAPLKLRLEIDGERSE-------- 54 Query: 61 IESVSDVPAAMGVAGGWLRDELRISPM-----AVGHRVVHGGPDYDRPVLIDHGVVARLE 115 +E +D AAM + +L + AVGHRVVHGG + V +D + LE Sbjct: 55 VEIDADPAAAMDRVLEQVLHQLEVGHAQGELCAVGHRVVHGGLHLAQAVRLDDAIETELE 114 Query: 116 RFVALAPLHQPNNLDPIRSLLANFPALPQVACFDTAFHRTHDAVADYYAIPYQFYVEGVR 175 LAPLHQP NL IR++ P LPQ A FDTAFH + DA+A +A+P + + EGV Sbjct: 115 NLAPLAPLHQPQNLRLIRAIARLRPGLPQTASFDTAFHASQDALARRFALPRRLHEEGVL 174 Query: 176 RYGFHGLSYEYVAKTLPHVAPEIAKGRVIVAHLGSGASMCALKGGRSIESTMGFTALDGL 235 RYGFHG+SY YVA + A A RV+VAHLG+GAS+CAL GRS++++ GF+ LDG+ Sbjct: 175 RYGFHGISYSYVAAEMRRQALPEAHARVVVAHLGNGASLCALHAGRSVDASTGFSTLDGV 234 Query: 236 PMGTRPGQIDPGVVLYLVSEKGMSPAKAQDFLYRDCGLKGLSGVSNDMRELEASEDPKAK 295 PMGTR G +D GV+LYL+ +GMS + +D LY GL G+SG+S D+R L+ S+D A+ Sbjct: 235 PMGTRCGALDAGVLLYLL-RQGMSLDELEDLLYHRSGLLGVSGLSADVRSLQQSQDSAAR 293 Query: 296 LAVDYFVYRVGLNAGMLAAALQGLDAFVFTAGIGENSMRIRARIADQLAWLGVTLDPTQN 355 A+D F R A LA+ L G+DA VFTAGIGE+ +RA I ++L WLGV LDP N Sbjct: 294 EALDLFALRCAGEAARLASTLGGIDALVFTAGIGEHDAAMRAAICERLGWLGVRLDPQAN 353 Query: 356 SRHARLISGSDSRIPVYVIPTDEELMIAQHTLSLLLDRSSSS 397 + HA IS +DS + VYVIPT+EE +IA +LLL ++ + Sbjct: 354 AAHAGRISRADSAVSVYVIPTNEEQVIADDAAALLLTSATGT 395 Lambda K H 0.320 0.137 0.403 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: 441 Number of extensions: 16 Number of successful extensions: 2 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: 397 Length adjustment: 31 Effective length of query: 373 Effective length of database: 366 Effective search space: 136518 Effective search space used: 136518 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 HSERO_RS01305 HSERO_RS01305 (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.29211.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-99 316.8 0.0 1.1e-98 316.6 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS01305 HSERO_RS01305 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS01305 HSERO_RS01305 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.6 0.0 1.1e-98 1.1e-98 4 403 .. 3 387 .. 1 389 [. 0.91 Alignments for each domain: == domain 1 score: 316.6 bits; conditional E-value: 1.1e-98 TIGR00016 4 kkilvlnaGssslkfalldaense.kvllsglverikleeariktvedgekkeeeklaiedheeavkk 70 +++l naGss +k ++ +++ +++ +g + + ++ dge+ e e+ +d ++a+++ lcl|FitnessBrowser__HerbieS:HSERO_RS01305 3 RLLLTFNAGSSTIKLGVFRLDGARaRKIGQGQLDLHLAP-LKLRLEIDGERSEVEID--ADPAAAMDR 67 578999************999854145789988865554.44555566655555444..577899*** PP TIGR00016 71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138 +l+++ ++ ++ + + e+ ++GHRvvhGg +++++v ++d + +++++++lAPlH p++l i+a+ lcl|FitnessBrowser__HerbieS:HSERO_RS01305 68 VLEQVLHQLEVGHAQGELCAVGHRVVHGGLHLAQAVRLDDAIETELENLAPLAPLHQPQNLRLIRAIA 135 ******9************************************************************* PP TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206 + ++ a FDtafH a +alP++l+ e gv rYGfHG+s++yv+ ++ + p+++ lcl|FitnessBrowser__HerbieS:HSERO_RS01305 136 --RLRPGLPQTASFDTAFHASQDALARRFALPRRLH-EEGVLRYGFHGISYSYVAAEMRRQ-ALPEAH 199 ..5556667***********************7765.66999*************998765.56789* PP TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetln 274 +++v+HlGnGas++a++ G+s+d s G+ L+G+ mGtR+G +D +++ yl +g+slde+e++l lcl|FitnessBrowser__HerbieS:HSERO_RS01305 200 ARVVVAHLGNGASLCALHAGRSVDASTGFSTLDGVPMGTRCGALDAGVLLYLLR-QGMSLDELEDLLY 266 ****************************************************86.79*********** PP TIGR00016 275 kksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGena 342 +sGllg+sgls+D+R + + + + a+ Al++++ R a ++ +++l g +Da+vFt+GiGe + lcl|FitnessBrowser__HerbieS:HSERO_RS01305 267 HRSGLLGVSGLSADVRSLQQSQ---DSAAREALDLFALRCAGEAARLASTLGG-IDALVFTAGIGEHD 330 ******************9988...45689*********************66.************** PP TIGR00016 343 aevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403 a +r+ ++e+l lG++ld++ n + + is +s+v v+viptnee via Da+ l lcl|FitnessBrowser__HerbieS:HSERO_RS01305 331 AAMRAAICERLGWLGVRLDPQANA----AHAGRISRADSAVSVYVIPTNEEQVIADDAAAL 387 *********************999....77889************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (397 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.36 // [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