Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_033106603.1 JF52_RS0110675 acetate kinase
Query= SwissProt::P77845 (397 letters) >NCBI__GCF_000763375.1:WP_033106603.1 Length = 406 Score = 363 bits (933), Expect = e-105 Identities = 193/403 (47%), Positives = 261/403 (64%), Gaps = 15/403 (3%) Query: 1 MALALVLNSGSSSIKFQLVNPENSAIDEPYVSGLVEQIGEPNGRIVLKI----EGEKYTL 56 M++ L++NSGSSS+K+ L++ + + P GL+E+IG+ I + +GE Sbjct: 1 MSVVLIINSGSSSLKYSLIDMDR---ESPLGEGLIERIGQDVSAISHTVRRRSDGEAAPT 57 Query: 57 --------ETPIADHSEGLNLAFDLMDQHNCGPSQLEITAVGHRVVHGGILFSAPELITD 108 E IA H E + + + H + AVGHRVVHGG F +P L+TD Sbjct: 58 VLDVTEKSERTIAAHDEAFAVMLEQFEAHGPALDEHAPVAVGHRVVHGGARFFSPTLVTD 117 Query: 109 EIVEMIRDLIPLAPLHNPANVDGIDVARKILPDVPHVAVFDTGFFHSLPPAAALYAINKD 168 + + I +L LAPLHNPAN+ GI AR + DVPHVAVFDT F +L P+A YAI+ Sbjct: 118 AVEQSIGELEVLAPLHNPANLAGIRAARAVFQDVPHVAVFDTAFHQTLKPSAYTYAIDAA 177 Query: 169 VAAEHGIRRYGFHGTSHEFVSKRVVEILEKPTEDINTITFHLGNGASMAAVQGGRAVDTS 228 A +H IRRYGFHGTSH++VS++ + L + + + FHLGNGAS+ A+ GGR+V+TS Sbjct: 178 FAEKHRIRRYGFHGTSHKYVSEQAADFLGRDLASLRQLVFHLGNGASVTAIGGGRSVETS 237 Query: 229 MGMTPLAGLVMGTRSGDIDPGIVFHLSRTAGMSIDEIDNLLNKKSGVKGLSGVNDFRELR 288 MG TPL GLVMGTRSGD+DP ++ H++R A SIDEID LLN +SG+KGL+G +D R++ Sbjct: 238 MGFTPLEGLVMGTRSGDLDPAVLVHIARVADYSIDEIDTLLNTRSGLKGLAGHSDMRDIL 297 Query: 289 EMIDNNDQDAWSAYNIYIHQLRRYLGSYMVALGRVDTIVFTAGVGENAQFVREDALAGLE 348 +D ++ A A+++YIH+LR Y G+Y+ LG VD I FTAGVGENA VR +AL+ L Sbjct: 298 AGVDAGEEAATLAFDVYIHRLRAYAGAYIAQLGGVDVISFTAGVGENAARVRAEALSTLG 357 Query: 349 MYGIEIDPERNALPNDGPRLISTDASKVKVFVIPTNEELAIAR 391 GIEID RN + R ISTD+S V V+PT+EEL IAR Sbjct: 358 FLGIEIDRARNEARSHSIRRISTDSSSASVLVVPTDEELEIAR 400 Lambda K H 0.318 0.137 0.395 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: 477 Number of extensions: 15 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: 397 Length of database: 406 Length adjustment: 31 Effective length of query: 366 Effective length of database: 375 Effective search space: 137250 Effective search space used: 137250 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_033106603.1 JF52_RS0110675 (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.981691.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-135 435.5 0.0 9.9e-135 435.3 0.0 1.1 1 NCBI__GCF_000763375.1:WP_033106603.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000763375.1:WP_033106603.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.3 0.0 9.9e-135 9.9e-135 4 401 .. 2 403 .. 1 406 [] 0.93 Alignments for each domain: == domain 1 score: 435.3 bits; conditional E-value: 9.9e-135 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv....edgek.......keeeklaiedhe 65 +++l++n+Gssslk++l+d+ e+ l +gl+eri + + i+ +dge +e+ + i++h+ NCBI__GCF_000763375.1:WP_033106603.1 2 SVVLIINSGSSSLKYSLIDMD-RESPLGEGLIERIGQDVSAISHTvrrrSDGEAaptvldvTEKSERTIAAHD 73 689*****************9.58999********999887765422212333222222224566678999** PP TIGR00016 66 eavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138 ea + +l++++++ l+e++ + ++GHRvvhGg +f + ++vtd v ++i ++ lAPlHnpa+l gi+a+ NCBI__GCF_000763375.1:WP_033106603.1 74 EAFAVMLEQFEAHGPALDEHAPV-AVGHRVVHGGARFFSPTLVTDAVEQSIGELEVLAPLHNPANLAGIRAAR 145 ***********876677777766.69*********************************************** PP TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnliv 211 v +++++vavFDtafHqt++ ay Ya+ + +++ +RrYGfHGtshkyv+++aa+ l++ l++l+ +v NCBI__GCF_000763375.1:WP_033106603.1 146 --AVFQDVPHVAVFDTAFHQTLKPSAYTYAIDAAFAEKHRIRRYGFHGTSHKYVSEQAADFLGRDLASLRQLV 216 ..888999***************************************************************** PP TIGR00016 212 cHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisg 284 HlGnGasv+a+ G+s++tsmG+tPLeGlvmGtRsGd+Dpa++ ++a + s+dei ++ln +sGl g++g NCBI__GCF_000763375.1:WP_033106603.1 217 FHLGNGASVTAIGGGRSVETSMGFTPLEGLVMGTRSGDLDPAVLVHIARVADYSIDEIDTLLNTRSGLKGLAG 289 ************************************************************************* PP TIGR00016 285 lssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlG 357 sD+Rdil+ +++g+e a+lA++vy+hR++ y g+yia+l g +D i Ft+G+Genaa vr+++l++l +lG NCBI__GCF_000763375.1:WP_033106603.1 290 -HSDMRDILAGVDAGEEAATLAFDVYIHRLRAYAGAYIAQLGG-VDVISFTAGVGENAARVRAEALSTLGFLG 360 .99**************************************76.***************************** PP TIGR00016 358 lkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401 +++d ++n+ ars++ + ist+ s+ vlv+pt+eel ia+ +l NCBI__GCF_000763375.1:WP_033106603.1 361 IEIDRARNE-ARSHSIRRISTDSSSASVLVVPTDEELEIARQTL 403 *********.99999*************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (406 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: 23.35 // [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