Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate 3607216 Dshi_0632 acetate kinase (RefSeq)
Query= curated2:B8EIS2 (404 letters) >FitnessBrowser__Dino:3607216 Length = 382 Score = 410 bits (1055), Expect = e-119 Identities = 214/394 (54%), Positives = 277/394 (70%), Gaps = 17/394 (4%) Query: 5 VITLNAGSSSIKFALFREGLTQEGSAKELTPMAIGLAEMVGEERRITVHDGAGAKIYEVK 64 ++TLNAGSSS+KFA++ +A + G + +G R+ V+ K Sbjct: 4 LLTLNAGSSSVKFAVYE-------AANAPLLIVAGEVDGLGPAARLIVNTNPATK----- 51 Query: 65 RTEHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTDEVLKYLHT 124 + HA AL ILA + +VV GHR+VHGG ++APV +T +V++ L Sbjct: 52 --RDLGPTDHAAALHAILAALRPILSGRQVVGVGHRIVHGGGAFTAPVELTPDVIEALEA 109 Query: 125 LIPLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRRFYDEGVRR 184 +PLAPLH+P+N+A + AR+A+P Q+ CFDTAFH HP+VND FALPRRFY+ GVRR Sbjct: 110 FVPLAPLHQPHNLAMVAAARQAFPDAVQIGCFDTAFHAGHPWVNDTFALPRRFYEAGVRR 169 Query: 185 YGFHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 244 YGFHGLSY+YI +LR P AAGRVV+AHLGNGASMCA+RDG SV S+MGF+ALDGLP Sbjct: 170 YGFHGLSYDYITDKLRADCPELAAGRVVIAHLGNGASMCAVRDGRSVGSTMGFSALDGLP 229 Query: 245 MGTRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEAADTLEAQQ 304 MGTRCGQLDPGV+LY+M E+ MS EIT +LY ESGL+GLSG SHDMR L+A+D A + Sbjct: 230 MGTRCGQLDPGVLLYMM-EQGMSREEITSILYEESGLQGLSGFSHDMRTLQASDDPRAAE 288 Query: 305 AIEYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGVELDRSANS 364 AI+Y+VFRIRRELG + AVL GIDA+VFCGGIGEN+ +R RV+EGM+++G+ LD AN+ Sbjct: 289 AIDYYVFRIRRELGAMTAVLGGIDALVFCGGIGENAAVIRARVIEGMDYLGLSLDAEANA 348 Query: 365 ANAEVISSERSRTRVFVIPTDEEGMIARHTLALL 398 NA +++ + VIPT+EE +IAR A L Sbjct: 349 RNATRVAT--GPVPILVIPTNEELVIARAVSAAL 380 Lambda K H 0.322 0.137 0.404 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: 467 Number of extensions: 15 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: 404 Length of database: 382 Length adjustment: 31 Effective length of query: 373 Effective length of database: 351 Effective search space: 130923 Effective search space used: 130923 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 3607216 Dshi_0632 (acetate kinase (RefSeq))
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.24946.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-107 346.1 0.0 1.4e-107 345.9 0.0 1.0 1 lcl|FitnessBrowser__Dino:3607216 Dshi_0632 acetate kinase (RefSeq Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607216 Dshi_0632 acetate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.9 0.0 1.4e-107 1.4e-107 4 400 .. 2 376 .. 1 381 [. 0.92 Alignments for each domain: == domain 1 score: 345.9 bits; conditional E-value: 1.4e-107 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkk 80 +++l lnaGsss+kfa+++a+n+ +++ g v+ + + +v+++ ++ l +dh++a++++l +l lcl|FitnessBrowser__Dino:3607216 2 SVLLTLNAGSSSVKFAVYEAANAPLLIVAGEVDGLGPAAR--LIVNTN-PATKRDLGPTDHAAALHAILAALRP--- 72 57899*****************9999*******9988777..434444.5666678889**************6... PP TIGR00016 81 ilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafH 157 + + ++ +GHR+vhGg ft v +t +v+++++ +++lAPlH p +l + a+ + ++a ++ +FDtafH lcl|FitnessBrowser__Dino:3607216 73 -ILSGRQVVGVGHRIVHGGGAFTAPVELTPDVIEALEAFVPLAPLHQPHNLAMVAAAR--QAFPDAVQIGCFDTAFH 146 .56778999************************************************9..5667788********** PP TIGR00016 158 qtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmG 234 p + +alP+++y e gvRrYGfHG+s+ y+t+++ l+ +++++HlGnGas++av++G+s+ +mG lcl|FitnessBrowser__Dino:3607216 147 AGHPWVNDTFALPRRFY-EAGVRRYGFHGLSYDYITDKLRADCPE-LAAGRVVIAHLGNGASMCAVRDGRSVGSTMG 221 *************9888.58*******************999887.8999*************************** PP TIGR00016 235 ltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyv 311 + L+Gl mGtR+G++Dp+++ y++e +g+s +ei+++l +sGl g+sg+s D+R++ + + +a+ A++ yv lcl|FitnessBrowser__Dino:3607216 222 FSALDGLPMGTRCGQLDPGVLLYMME-QGMSREEITSILYEESGLQGLSGFSHDMRTLQASD---DPRAAEAIDYYV 294 ************************98.59****************************98766...7789******** PP TIGR00016 312 hRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlvi 388 Ri++ +g+++a l g +Da+vF gGiGenaa +r++v+e+++ lGl ld e n + + ++ + v +lvi lcl|FitnessBrowser__Dino:3607216 295 FRIRRELGAMTAVLGG-IDALVFCGGIGENAAVIRARVIEGMDYLGLSLDAEANA----RNATRVA--TGPVPILVI 364 **************76.*************************************9....3333444..599****** PP TIGR00016 389 ptneelviaeDa 400 ptneelvia+ + lcl|FitnessBrowser__Dino:3607216 365 PTNEELVIARAV 376 ********9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (382 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.64 // [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