Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 7024360 Shewana3_1552 acetate kinase (RefSeq)
Query= BRENDA::E3W769 (401 letters) >FitnessBrowser__ANA3:7024360 Length = 399 Score = 683 bits (1762), Expect = 0.0 Identities = 336/399 (84%), Positives = 371/399 (92%), Gaps = 1/399 (0%) Query: 1 MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60 MS+KLVLVLNCGSSSLKFA+IDAQ+GDD+ISGLAECFGLEDSRIKWK NG K+E+ LGAF Sbjct: 1 MSNKLVLVLNCGSSSLKFAVIDAQTGDDQISGLAECFGLEDSRIKWKINGEKHESSLGAF 60 Query: 61 TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120 TAHREAVEF IVN ILA PELAAQI+A+GHRIVHGGEKFTRSVII VI+GIE+C+SL Sbjct: 61 TAHREAVEF-IVNKILAGQPELAAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSL 119 Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180 APLHNPAHLIGIRAAIASFP+LPQV VFDTAFHQ+MPE+AYIYALPYKLYREH IRRYGM Sbjct: 120 APLHNPAHLIGIRAAIASFPKLPQVAVFDTAFHQSMPERAYIYALPYKLYREHGIRRYGM 179 Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240 HGTSH +V REAAKVL K +++ NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG Sbjct: 180 HGTSHLFVSREAAKVLNKPLEETNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239 Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300 TRCGDLDPSII+HLV QLGYTL+EVNNL+NKQSGLLGISELTNDCRGIEEGY DGHKGAT Sbjct: 240 TRCGDLDPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGAT 299 Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360 LAL+IFCYRLAKYIASYTVPLGRLDA++FTGGIGENS++IREKVLN+L+IFNF VD N Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAVVFTGGIGENSDIIREKVLNMLQIFNFHVDSERN 359 Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLIT 399 KAARFG++G+IT + +AMVIPTNEEWVIAED+IKLIT Sbjct: 360 KAARFGKKGIITTDNSTVAMVIPTNEEWVIAEDSIKLIT 398 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: 630 Number of extensions: 17 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 7024360 Shewana3_1552 (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.17477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-171 555.3 0.2 3.9e-171 555.2 0.2 1.0 1 lcl|FitnessBrowser__ANA3:7024360 Shewana3_1552 acetate kinase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024360 Shewana3_1552 acetate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.2 0.2 3.9e-171 3.9e-171 2 404 .. 2 397 .. 1 398 [. 0.98 Alignments for each domain: == domain 1 score: 555.2 bits; conditional E-value: 3.9e-171 TIGR00016 2 kskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 ++k++lvln+Gssslkfa++da++++ +sgl+e++ le++rik++ +gek+e+ a+++h+eav++++n++ + lcl|FitnessBrowser__ANA3:7024360 2 SNKLVLVLNCGSSSLKFAVIDAQTGDDQ-ISGLAECFGLEDSRIKWKINGEKHESSLGAFTAHREAVEFIVNKILA- 76 6799********************9999.9*********************************************7. PP TIGR00016 79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDta 155 ++ ++i+++GHR+vhGgekft svi++++v+k+i++ s+lAPlHnpa+l+gi+a+ +k ++vavFDta lcl|FitnessBrowser__ANA3:7024360 77 -GQPELAAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSLAPLHNPAHLIGIRAAI--ASFPKLPQVAVFDTA 150 .559********************************************************..6677889******** PP TIGR00016 156 fHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidts 232 fHq +pe+ay+YalPy+ly+e+g+RrYG+HGtsh +v+++aak+lnkpl++ n+i +HlGnGasv+avk Gks+dts lcl|FitnessBrowser__ANA3:7024360 151 FHQSMPERAYIYALPYKLYREHGIRRYGMHGTSHLFVSREAAKVLNKPLEETNVICAHLGNGASVTAVKGGKSVDTS 227 ***************************************************************************** PP TIGR00016 233 mGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkv 309 mGltPLeGlvmGtR+Gd+Dp+ii +l ++lg +l+e+++++nk+sGllgis+l++D+R i++ +++g++ a+lAl++ lcl|FitnessBrowser__ANA3:7024360 228 MGLTPLEGLVMGTRCGDLDPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGATLALEI 304 ***************************************************************************** PP TIGR00016 310 yvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvl 386 +++R+akyi++y+ l g+lDa+vFtgGiGen+ +re+vl+ l+++ +++d+e+n+aar+gk+++i+t++s+v ++ lcl|FitnessBrowser__ANA3:7024360 305 FCYRLAKYIASYTVPL-GRLDAVVFTGGIGENSDIIREKVLNMLQIFNFHVDSERNKAARFGKKGIITTDNSTV-AM 379 ****************.67***************************************************9998.58 PP TIGR00016 387 viptneelviaeDalrla 404 viptnee+viaeD+++l+ lcl|FitnessBrowser__ANA3:7024360 380 VIPTNEEWVIAEDSIKLI 397 9**************997 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.33 // [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