Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 5209945 Shew_2393 acetate kinase (RefSeq)
Query= BRENDA::E3W769 (401 letters) >FitnessBrowser__PV4:5209945 Length = 398 Score = 667 bits (1721), Expect = 0.0 Identities = 328/398 (82%), Positives = 362/398 (90%), Gaps = 1/398 (0%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS+KLVLVLNCGSSSLKFAIIDA +GDD+ISGLAECFGLEDSRIKWK +G K E+KLGAF Sbjct: 1 MSNKLVLVLNCGSSSLKFAIIDALTGDDQISGLAECFGLEDSRIKWKVDGNKFESKLGAF 60 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 TAHREAVEF IV IL ++P++AAQI+AIGHR+VHGGEKFT SV+I VI GIEDCA+L Sbjct: 61 TAHREAVEF-IVKEILGQYPDVAAQIQAIGHRVVHGGEKFTHSVVIDDSVIAGIEDCAAL 119 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQTMPE+A++YALPYKLYREH IRRYGM Sbjct: 120 APLHNPAHLIGIRAAQASFPGLPQVAVFDTAFHQTMPERAFVYALPYKLYREHGIRRYGM 179 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH +V REAAK LGK++ D NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG Sbjct: 180 HGTSHLFVSREAAKALGKELADTNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TRCGD+DPSII+HLV +LGYTLDEVNNL+NKQSGLLGISELTNDCRGIEEGY +GHKGAT Sbjct: 240 TRCGDIDPSIIYHLVDRLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGAT 299 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LAL+IFCYRLAKYIASYTVPLGRLDA++FTGGIGENS+LIREKVLNLL IFNF+VD N Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDALVFTGGIGENSDLIREKVLNLLAIFNFEVDPARN 359 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398 +AARFG QG IT P+AMVIPTNEEWVIAEDA+ L+ Sbjct: 360 QAARFGNQGQITTDNGPVAMVIPTNEEWVIAEDAVSLL 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: 600 Number of extensions: 22 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 5209945 Shew_2393 (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.5006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-168 544.0 0.0 1.1e-167 543.8 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209945 Shew_2393 acetate kinase (RefSeq Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209945 Shew_2393 acetate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 543.8 0.0 1.1e-167 1.1e-167 2 404 .. 2 397 .. 1 398 [] 0.97 Alignments for each domain: == domain 1 score: 543.8 bits; conditional E-value: 1.1e-167 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdk 79 ++k++lvln+Gssslkfa++da +++ +sgl+e++ le++rik+++dg+k e++ a+++h+eav+++++++ lcl|FitnessBrowser__PV4:5209945 2 SNKLVLVLNCGSSSLKFAIIDALTGDDQ-ISGLAECFGLEDSRIKWKVDGNKFESKLGAFTAHREAVEFIVKEILG-- 76 6799*******************99999.9*********************************************7.. PP TIGR00016 80 kilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafH 157 + + ++i++iGHRvvhGgekft+sv+++d+v+++i+d + lAPlHnpa+l+gi+a+++++ + ++vavFDtafH lcl|FitnessBrowser__PV4:5209945 77 QYPDVAAQIQAIGHRVVHGGEKFTHSVVIDDSVIAGIEDCAALAPLHNPAHLIGIRAAQASF--PGLPQVAVFDTAFH 152 5699*******************************************************555..5567********** PP TIGR00016 158 qtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmGl 235 qt+pe+a++YalPy+ly+e+g+RrYG+HGtsh +v+++aak l+k+l+d n+i +HlGnGasv+avk Gks+dtsmGl lcl|FitnessBrowser__PV4:5209945 153 QTMPERAFVYALPYKLYREHGIRRYGMHGTSHLFVSREAAKALGKELADTNVICAHLGNGASVTAVKGGKSVDTSMGL 230 ****************************************************************************** PP TIGR00016 236 tPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhR 313 tPLeGlvmGtR+GdiDp+ii +l ++lg +lde+++++nk+sGllgis+l++D+R i++ ++eg++ a+lAl+++++R lcl|FitnessBrowser__PV4:5209945 231 TPLEGLVMGTRCGDIDPSIIYHLVDRLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGATLALEIFCYR 308 ****************************************************************************** PP TIGR00016 314 iakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptn 391 +akyi++y+ l g+lDa+vFtgGiGen+ +re+vl+ l+++ +++d+++n+aar+g+++ i+t+++ v ++viptn lcl|FitnessBrowser__PV4:5209945 309 LAKYIASYTVPL-GRLDALVFTGGIGENSDLIREKVLNLLAIFNFEVDPARNQAARFGNQGQITTDNGPV-AMVIPTN 384 ************.67***************************************************9998.589**** PP TIGR00016 392 eelviaeDalrla 404 ee+viaeDa+ l lcl|FitnessBrowser__PV4:5209945 385 EEWVIAEDAVSLL 397 *********9886 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: 00:00:00.01 # Mc/sec: 11.04 // [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