Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_012277679.1 SHAL_RS13495 acetate kinase
Query= BRENDA::E3W769 (401 letters) >NCBI__GCF_000019185.1:WP_012277679.1 Length = 398 Score = 655 bits (1691), Expect = 0.0 Identities = 327/398 (82%), Positives = 356/398 (89%), Gaps = 1/398 (0%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS+KLVLVLNCGSSSLKFA+IDA SGDD+ISGLAECFGLEDSRIKWK NG K+EA LGAF Sbjct: 1 MSNKLVLVLNCGSSSLKFAVIDAISGDDQISGLAECFGLEDSRIKWKVNGQKSEASLGAF 60 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 TAHREAVE+ IVN+IL HPE+AA+I+AIGHR+VHGGEKFT SVII VI GIEDCA+L Sbjct: 61 TAHREAVEY-IVNDILGAHPEIAAEIQAIGHRVVHGGEKFTHSVIIDESVIHGIEDCATL 119 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQTMPEKAYIYALPYKLYRE++IRRYGM Sbjct: 120 APLHNPAHLIGIRAAQASFPALPQVAVFDTAFHQTMPEKAYIYALPYKLYRENAIRRYGM 179 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH ++ REAA LGKD D N+ICAHLGNGASV AIKGGKSVDTSMGLTPLEGLVMG Sbjct: 180 HGTSHLFISREAAAALGKDEADTNIICAHLGNGASVTAIKGGKSVDTSMGLTPLEGLVMG 239 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TRCGD+DPS+IFHLV +LGYTLDEV ++LNKQSGLLGISELTNDCRGIEEG+ +GHKGAT Sbjct: 240 TRCGDVDPSVIFHLVNRLGYTLDEVESVLNKQSGLLGISELTNDCRGIEEGFENGHKGAT 299 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LAL+IFCYRLAKYIASYTVPL RLDA++FTGGIGENSNLIREKVLN L IFNF VD N Sbjct: 300 LALEIFCYRLAKYIASYTVPLERLDAVVFTGGIGENSNLIREKVLNSLAIFNFNVDAERN 359 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398 AARFG G IT +AMVIPTNEEWVIA+DAI+LI Sbjct: 360 AAARFGNGGKITTDEGTVAMVIPTNEEWVIAQDAIELI 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: 602 Number of extensions: 23 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: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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 WP_012277679.1 SHAL_RS13495 (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.2223215.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-167 541.4 0.1 6.4e-167 541.3 0.1 1.0 1 NCBI__GCF_000019185.1:WP_012277679.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019185.1:WP_012277679.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 541.3 0.1 6.4e-167 6.4e-167 2 404 .. 2 397 .. 1 398 [] 0.97 Alignments for each domain: == domain 1 score: 541.3 bits; conditional E-value: 6.4e-167 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 ++k++lvln+Gssslkfa++da +++ +sgl+e++ le++rik++++g+k e+ a+++h+eav+ ++n NCBI__GCF_000019185.1:WP_012277679.1 2 SNKLVLVLNCGSSSLKFAVIDAISGDDQ-ISGLAECFGLEDSRIKWKVNGQKSEASLGAFTAHREAVEYIVND 73 6799*******************99999.9******************************************* PP TIGR00016 75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147 + + + +ei++iGHRvvhGgekft+svi++++v+++i+d + lAPlHnpa+l+gi+a+++ + + NCBI__GCF_000019185.1:WP_012277679.1 74 ILG--AHPEIAAEIQAIGHRVVHGGEKFTHSVIIDESVIHGIEDCATLAPLHNPAHLIGIRAAQA--SFPALP 142 **7..55999******************************************************5..556678 PP TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220 +vavFDtafHqt+pe+ay+YalPy+ly+e+ +RrYG+HGtsh +++++aa l+k ++d n+i +HlGnGasv NCBI__GCF_000019185.1:WP_012277679.1 143 QVAVFDTAFHQTMPEKAYIYALPYKLYRENAIRRYGMHGTSHLFISREAAAALGKDEADTNIICAHLGNGASV 215 ************************************************************************* PP TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293 +a+k Gks+dtsmGltPLeGlvmGtR+Gd+Dp++i++l ++lg +lde+e++lnk+sGllgis+l++D+R i+ NCBI__GCF_000019185.1:WP_012277679.1 216 TAIKGGKSVDTSMGLTPLEGLVMGTRCGDVDPSVIFHLVNRLGYTLDEVESVLNKQSGLLGISELTNDCRGIE 288 ************************************************************************* PP TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366 + e+g++ a+lAl+++++R+akyi++y+ le lDa+vFtgGiGen+ +re+vl++l+++ +++d e+n NCBI__GCF_000019185.1:WP_012277679.1 289 EGFENGHKGATLALEIFCYRLAKYIASYTVPLER-LDAVVFTGGIGENSNLIREKVLNSLAIFNFNVDAERNA 360 ********************************76.************************************** PP TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrla 404 aar+g+ + i+t+e++v ++viptnee+via+Da++l+ NCBI__GCF_000019185.1:WP_012277679.1 361 AARFGNGGKITTDEGTV-AMVIPTNEEWVIAQDAIELI 397 ***********999987.689**************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (398 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: 00:00:00.00 # Mc/sec: 16.41 // [ok]
This GapMind analysis is from Sep 24 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