Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 6937325 Sama_1495 acetate kinase (RefSeq)
Query= BRENDA::E3W769 (401 letters) >FitnessBrowser__SB2B:6937325 Length = 399 Score = 672 bits (1733), Expect = 0.0 Identities = 332/398 (83%), Positives = 362/398 (90%), Gaps = 1/398 (0%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS+ LVLVLNCGSSSLKFAI+DA +GD+KISGLAECFGLE++RIKWK G K+EA LGAF Sbjct: 1 MSNTLVLVLNCGSSSLKFAILDATNGDEKISGLAECFGLENARIKWKLRGEKHEASLGAF 60 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 +AHREAVE+ IVN IL PEL Q+ AIGHRIVHGGEKFT SVII V++GIEDCASL Sbjct: 61 SAHREAVEY-IVNKILVNEPELKGQLIAIGHRIVHGGEKFTHSVIIDDAVLKGIEDCASL 119 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQ+MP++AYIYALPYKLYREH IRRYGM Sbjct: 120 APLHNPAHLIGIRAAQASFPSLPQVAVFDTAFHQSMPDRAYIYALPYKLYREHGIRRYGM 179 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH +V REAAK LGKDV D NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG Sbjct: 180 HGTSHLFVSREAAKALGKDVNDTNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TRCGDLDPSII+HLV QLGYTLDEVNNL+NKQSGLLGISELTNDCRGIEEGY +GHKGAT Sbjct: 240 TRCGDLDPSIIYHLVHQLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGAT 299 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LAL+IFCYRLAKYIASYTVPLGRLDAI+FTGGIGENS+LIREKVLNLLEIF F+VD N Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAIVFTGGIGENSDLIREKVLNLLEIFKFEVDSERN 359 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398 KAARFG QGVIT+ G+PIAMVIPTNEEWVIAED+++L+ Sbjct: 360 KAARFGNQGVITKEGSPIAMVIPTNEEWVIAEDSLRLV 397 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: 610 Number of extensions: 24 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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 6937325 Sama_1495 (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.2391576.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-169 548.6 0.0 4.4e-169 548.4 0.0 1.0 1 FitnessBrowser__SB2B:6937325 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6937325 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.4 0.0 4.4e-169 4.4e-169 2 404 .. 2 397 .. 1 398 [. 0.97 Alignments for each domain: == domain 1 score: 548.4 bits; conditional E-value: 4.4e-169 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkkil 82 +++++lvln+Gssslkfa+lda+n++++ +sgl+e++ le+arik++ gek+e+ a+++h+eav+ ++n++ ++ FitnessBrowser__SB2B:6937325 2 SNTLVLVLNCGSSSLKFAILDATNGDEK-ISGLAECFGLENARIKWKLRGEKHEASLGAFSAHREAVEYIVNKILVNE--P 79 6789************************.9********************************************9755..9 PP TIGR00016 83 kelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafHqtipee 163 +++ ++ +iGHR+vhGgekft+svi++d vlk+i+d ++lAPlHnpa+l+gi+a++ ++ ++vavFDtafHq +p++ FitnessBrowser__SB2B:6937325 80 ELKGQLIAIGHRIVHGGEKFTHSVIIDDAVLKGIEDCASLAPLHNPAHLIGIRAAQ--ASFPSLPQVAVFDTAFHQSMPDR 158 99******************************************************..6667778**************** PP TIGR00016 164 aylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmG 244 ay+YalPy+ly+e+g+RrYG+HGtsh +v+++aak l+k ++d n+i +HlGnGasv+avk Gks+dtsmGltPLeGlvmG FitnessBrowser__SB2B:6937325 159 AYIYALPYKLYREHGIRRYGMHGTSHLFVSREAAKALGKDVNDTNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239 ********************************************************************************* PP TIGR00016 245 tRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiasl 325 tR+Gd+Dp+ii +l ++lg +lde+++++nk+sGllgis+l++D+R i++ ++eg++ a+lAl+++++R+akyi++y+ l FitnessBrowser__SB2B:6937325 240 TRCGDLDPSIIYHLVHQLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGATLALEIFCYRLAKYIASYTVPL 320 ********************************************************************************* PP TIGR00016 326 egelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404 g+lDaivFtgGiGen+ +re+vl+ le++ +++d+e+n+aar+g+++vi++e ++ ++viptnee+viaeD+lrl+ FitnessBrowser__SB2B:6937325 321 -GRLDAIVFTGGIGENSDLIREKVLNLLEIFKFEVDSERNKAARFGNQGVITKE-GSPIAMVIPTNEEWVIAEDSLRLV 397 .67************************************************955.5556899**************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (399 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 22.88 // [ok]
This GapMind analysis is from Apr 09 2024. 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