Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF3154 Psest_3213 acetate kinase
Query= BRENDA::E3W769 (401 letters) >FitnessBrowser__psRCH2:GFF3154 Length = 395 Score = 384 bits (987), Expect = e-111 Identities = 204/401 (50%), Positives = 269/401 (67%), Gaps = 7/401 (1%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS + +LV+NCGSSS+KFA+++ + GLAEC G ++ I ++ GK K+ Sbjct: 1 MSARNILVINCGSSSIKFALVNEAQATFPLQGLAECIGSPEAVIHFESAAGKESVKVPN- 59 Query: 61 TAHREAVEFFIVNNILAEHPELAA-QIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCAS 119 H+ A+ IL E A + IGHR+VHGGEKF S ++ E + GIE Sbjct: 60 ADHQAALA-----QILPRVEEAAGGHLDGIGHRVVHGGEKFFASSLLNDETLAGIEANIQ 114 Query: 120 LAPLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYG 179 LAPLHNPA+L GI AAI FP+LPQV VFDTAFHQTMPE AY YA+P LY+EH +RRYG Sbjct: 115 LAPLHNPANLSGIHAAINLFPELPQVGVFDTAFHQTMPEHAYRYAVPDVLYKEHGVRRYG 174 Query: 180 MHGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVM 239 HGTSH +V + AA++ G V++ + + AHLGNG S A+ G+S DTSMGLTPLEGLVM Sbjct: 175 FHGTSHRFVSKRAAEMAGVPVENSSWLVAHLGNGCSTCAVVNGESRDTSMGLTPLEGLVM 234 Query: 240 GTRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGA 299 GTR GD+DPS+ L K LG+ L +++N+LNK+SGL G+S L+ND R + + + GH GA Sbjct: 235 GTRSGDVDPSLHNFLNKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLADARNAGHPGA 294 Query: 300 TLALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDIL 359 LA D+FCYRLAK +A+ + L +LD ++FTGGIGENS+ +RE+ L L++F FK+D Sbjct: 295 VLAFDVFCYRLAKSLAAMSCALPQLDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEA 354 Query: 360 NKAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400 N G G I AG+P MV+PTNEE IA D + L+ A Sbjct: 355 NARCTRGVAGEIQAAGSPRIMVVPTNEERQIALDTLALLDA 395 Lambda K H 0.321 0.139 0.409 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: 487 Number of extensions: 19 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: 401 Length of database: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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 GFF3154 Psest_3213 (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.18611.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-143 464.9 0.0 1.1e-143 464.7 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3154 Psest_3213 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3154 Psest_3213 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.7 0.0 1.1e-143 1.1e-143 2 403 .. 2 392 .. 1 394 [. 0.95 Alignments for each domain: == domain 1 score: 464.7 bits; conditional E-value: 1.1e-143 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 + + ilv+n+Gsss+kfal++ ++ + l+gl+e+i ++ea+i e++ ke+ k+ +dh++a++++l +++ lcl|FitnessBrowser__psRCH2:GFF3154 2 SARNILVINCGSSSIKFALVNEAQ-ATFPLQGLAECIGSPEAVIH-FESAAGKESVKVPNADHQAALAQILPRVE 74 5678******************96.55669************666.6777788999999**************** PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvav 151 + +++ iGHRvvhGgekf s +++de+l++i+ ++lAPlHnpa+l+gi+a+ + ++ ++v v lcl|FitnessBrowser__psRCH2:GFF3154 75 E-----AAGGHLDGIGHRVVHGGEKFFASSLLNDETLAGIEANIQLAPLHNPANLSGIHAAI--NLFPELPQVGV 142 5.....67899***************************************************..6667788**** PP TIGR00016 152 FDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknG 226 FDtafHqt+pe+ay Ya+P lyke+gvRrYGfHGtsh++v++raa++ + p++++ +v+HlGnG s +av nG lcl|FitnessBrowser__psRCH2:GFF3154 143 FDTAFHQTMPEHAYRYAVPDVLYKEHGVRRYGFHGTSHRFVSKRAAEMAGVPVENSSWLVAHLGNGCSTCAVVNG 217 *************************************************************************** PP TIGR00016 227 ksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegne 301 +s dtsmGltPLeGlvmGtRsGd+Dp++ ++l++tlg l++i ++lnk+sGl g+sgls+D+R++ d+ ++g+ lcl|FitnessBrowser__psRCH2:GFF3154 218 ESRDTSMGLTPLEGLVMGTRSGDVDPSLHNFLNKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLADARNAGHP 292 *************************************************************************** PP TIGR00016 302 eaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvi 376 a lA++v+++R+ak ++++ +l + lD++vFtgGiGen++ vre++le+l+++G+kld e n ++++g + i lcl|FitnessBrowser__psRCH2:GFF3154 293 GAVLAFDVFCYRLAKSLAAMSCALPQ-LDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEANARCTRGVAGEI 366 ************************66.************************************************ PP TIGR00016 377 steeskvkvlviptneelviaeDalrl 403 s +++v+ptnee ia D+l l lcl|FitnessBrowser__psRCH2:GFF3154 367 QAAGS-PRIMVVPTNEERQIALDTLAL 392 96655.689**************9877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (395 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: 12.04 // [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