Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate Synpcc7942_2079 Synpcc7942_2079 acetate kinase
Query= curated2:Q8YU00 (405 letters) >FitnessBrowser__SynE:Synpcc7942_2079 Length = 393 Score = 337 bits (864), Expect = 4e-97 Identities = 189/405 (46%), Positives = 256/405 (63%), Gaps = 19/405 (4%) Query: 1 MKVLILNAGSSSQKSCLYEIPDDALLSEAPQPLWEGKVNWTQDRSVAEIEVKTARGETLH 60 +++L NAGSSS K +EI A E P+W+ +++W DR+ T G+ + Sbjct: 1 LQLLTFNAGSSSYKLSGFEITTAA---EQTDPVWQVQIDWKTDRAAT----LTQPGQPV- 52 Query: 61 ESIYGDSRQAHVTYMLYTLSRGATKVIGQLSEIDVVGHRVVHGGQNYRHSVIITEEVKQA 120 + + R+A + L TL S I V HRVVHGGQ +V+ T E+K Sbjct: 53 QMLDSSDRRAWLEIALETLP--------DRSAIAAVVHRVVHGGQQQAPAVV-TPELKAT 103 Query: 121 IAKLSNLAPAHNPAALEGIEAIEKSLG-DVPQVAVFDTGFHATLPDAAAIYPGPFEWVEQ 179 IA +NLAP HNP L GIE +E+ G +PQ+AVFDT FH +P AAAIY GP+ W EQ Sbjct: 104 IAAAANLAPLHNPLNLAGIEQMEQLFGLAMPQIAVFDTAFHQQMPVAAAIYGGPYHWWEQ 163 Query: 180 GIRRYGFHGISHQYCSARAAQILGRDLASLRIITCHLGNGCSLAAIKNGRSIDTTMGFTP 239 G RRYGFHGISHQY + R AQ+ R L++L+++T HLGNGCSLAAI+NG S+DT+MGF+P Sbjct: 164 GYRRYGFHGISHQYLAERCAQLSDRSLSNLQLVTAHLGNGCSLAAIRNGHSVDTSMGFSP 223 Query: 240 LDGLMMGSRSGAIDPGIIVHLMRQSDYSAERLDYVLNKASGLRGISGVSSDLPQVIEAIT 299 L+GL+MGSRSG +DPG+++HL++Q D S +L VLN+ SGL G+SG S+D+ + A Sbjct: 224 LEGLVMGSRSGTVDPGLLLHLLQQPDCSPSQLSTVLNQQSGLLGLSGRSNDVRALAIAAD 283 Query: 300 QGNYRAQLAWDMYVHRLRSGIGSMLASLGGLDVLVFTAGVGEKSAGIRQAACEAFGFLGL 359 G+ R+QLA + H LR +G+MLASL LD LVF G+GE + A CE F + + Sbjct: 284 AGDQRSQLALAAFTHSLRRHLGAMLASLTRLDALVFAGGIGENYRSLWPAVCEHFAGMPI 343 Query: 360 KLDPEKNQNKPVDIDIATADSTVRVLVIHTQEDWAIAQQCWHLLK 404 +LDPE D I+T DS + V VIH++EDW + Q LL+ Sbjct: 344 RLDPEA-MAVAGDRRISTPDSAITVWVIHSREDWQMVQLALPLLR 387 Lambda K H 0.319 0.135 0.400 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: 428 Number of extensions: 15 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: 405 Length of database: 393 Length adjustment: 31 Effective length of query: 374 Effective length of database: 362 Effective search space: 135388 Effective search space used: 135388 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 Synpcc7942_2079 Synpcc7942_2079 (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.30451.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-110 353.1 0.0 1e-109 352.9 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2079 Synpcc7942_2079 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2079 Synpcc7942_2079 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.9 0.0 1e-109 1e-109 6 400 .. 3 382 .. 1 387 [. 0.91 Alignments for each domain: == domain 1 score: 352.9 bits; conditional E-value: 1e-109 TIGR00016 6 ilvlnaGssslkfalldaensekv...llsglverikleeariktvedgekkeeeklaiedheeavkkl 71 +l naGsss k + ++ +++ + +++ +++ + r t+++ + ++l+ +d+++ ++ lcl|FitnessBrowser__SynE:Synpcc7942_2079 3 LLTFNAGSSSYKLSGFEITTAAEQtdpVWQVQIDWKT---DRAATLTQP-GQPVQMLDSSDRRAWLEIA 67 7899*********999999866652335555555543...333444444.4667889999999999999 PP TIGR00016 72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140 l+tl + s ia++ HRvvhGg++ + + +vt e + i+ +++lAPlHnp +l gie++ +l lcl|FitnessBrowser__SynE:Synpcc7942_2079 68 LETLP-------DRSAIAAVVHRVVHGGQQQAPA-VVTPELKATIAAAANLAPLHNPLNLAGIEQMEQL 128 99999.......4799************998766.689*****************************88 PP TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnl 209 + l +++avFDtafHq +p a++Y+ Py++++ +g RrYGfHG+sh+y+++r a+l +++l +l+l lcl|FitnessBrowser__SynE:Synpcc7942_2079 129 FGLAM-PQIAVFDTAFHQQMPVAAAIYGGPYHWWE-QGYRRYGFHGISHQYLAERCAQLSDRSLSNLQL 195 77665.***************************96.699****************************** PP TIGR00016 210 ivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksG 278 +++HlGnG s++a++nG+s+dtsmG+ PLeGlvmG+RsG +Dp+++ +l ++ + s +++ ++ln++sG lcl|FitnessBrowser__SynE:Synpcc7942_2079 196 VTAHLGNGCSLAAIRNGHSVDTSMGFSPLEGLVMGSRSGTVDPGLLLHLLQQPDCSPSQLSTVLNQQSG 264 ********************************************************************* PP TIGR00016 279 llgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevre 347 llg+sg s+D+R + + ++g+++++lAl ++h +++++g+++asl +lDa+vF gGiGen ++ lcl|FitnessBrowser__SynE:Synpcc7942_2079 265 LLGLSGRSNDVRALAIAADAGDQRSQLALAAFTHSLRRHLGAMLASL-TRLDALVFAGGIGENYRSLWP 332 ***********************************************.55******************* PP TIGR00016 348 lvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDa 400 v+e+++ + ++ld+e ++ ist++s+++v vi+ e++ +++ a lcl|FitnessBrowser__SynE:Synpcc7942_2079 333 AVCEHFAGMPIRLDPEAMA---VAGDRRISTPDSAITVWVIHSREDWQMVQLA 382 ****************998...789999*******************999865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (393 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: 00:00:00.02 # Mc/sec: 7.62 // [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