Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_036261519.1 DL86_RS11535 acetate/propionate family kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_000746085.1:WP_036261519.1 Length = 400 Score = 286 bits (733), Expect = 6e-82 Identities = 166/398 (41%), Positives = 244/398 (61%), Gaps = 23/398 (5%) Query: 4 IIAINAGSSSLKFQLFEMPSE--TVLTKGLVERIGIADSVFTISVNG-----EKNTEVTD 56 ++ +NAGSSS+KF LFE+ L GLVE +G + G + T+ D Sbjct: 5 VVTLNAGSSSIKFALFELNGREPVALAVGLVEMLGEQRRLKARDGGGAPIHEDAWTDAGD 64 Query: 57 IPDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISE 116 P H A++ +L G + N + GHRVVHGG F L+TDE ++ +E +S Sbjct: 65 APFHTEALRRVL--AWRLGAFPEANVV-AAGHRVVHGGVYFDAPALVTDEVLRILESLSP 121 Query: 117 LAPLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYG 176 LAPLH P NI GI A +E P+V VA FDTAFH+ P + +++LP ++Y++ G+R+YG Sbjct: 122 LAPLHQPHNIAGILAAREAWPHVRQVACFDTAFHRAHPFVNDVFALPRKFYDE-GVRRYG 180 Query: 177 FHGTSHKYVTERAAELLGRPLKDL-RLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVA 235 FHG S++YVTE+ ++ PL R++ HLGNGAS+ A+ G S+ +SMGFT L G+ Sbjct: 181 FHGLSYEYVTEKLQQV--APLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 238 Query: 236 MGTRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNER 295 MGTR G +DP ++ Y+M++ +A+ + + L ++SGL G+SG S D+R++ E ++R Sbjct: 239 MGTRCGQLDPGVVLYLMQEMKMSAEAIADLLYRESGLKGLSGVSHDMREL-----EASDR 293 Query: 296 AET--ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWD 353 E A+E F RI + +G AA + G+DA++F GIGE++ VRERVL G+E++G+ D Sbjct: 294 PEARQAIEYFVFRIRRELGGLAAVLEGLDAMVFCGGIGEHAWRVRERVLEGMEWIGIELD 353 Query: 354 PALNNVRGEEAFISYPHSPVKVMIIPTDEEVMIARDVV 391 N R E IS S V+V +IPTDEE MIAR + Sbjct: 354 RTAN--RASEQVISSQRSRVRVFVIPTDEEAMIARQTL 389 Lambda K H 0.317 0.136 0.381 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: 340 Number of extensions: 12 Number of successful extensions: 6 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: 395 Length of database: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_036261519.1 DL86_RS11535 (acetate/propionate family 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.662794.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-114 369.3 0.0 1.2e-114 369.1 0.0 1.0 1 NCBI__GCF_000746085.1:WP_036261519.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000746085.1:WP_036261519.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.1 0.0 1.2e-114 1.2e-114 4 402 .. 3 390 .. 1 393 [. 0.90 Alignments for each domain: == domain 1 score: 369.1 bits; conditional E-value: 1.2e-114 TIGR00016 4 kkilvlnaGssslkfalldaensekv.llsglverikleeariktvedg.....ekkeeeklaiedheeavkk 70 + ++ lnaGsss+kfal++ ++ e v l+ glve++ + +k g e+ ++ + + h+ea+++ NCBI__GCF_000746085.1:WP_036261519.1 3 RHVVTLNAGSSSIKFALFELNGREPVaLAVGLVEMLGEQRR-LKARDGGgapihEDAWTDAGDAPFHTEALRR 74 67999****************988777999****9987766.4444333111112333445556668888888 PP TIGR00016 71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143 +l ++++ + GHRvvhGg +f ++vtdevl+ ++ +s+lAPlH p ++ gi a+ + NCBI__GCF_000746085.1:WP_036261519.1 75 VLAWRLG----AFPEANVVAAGHRVVHGGVYFDAPALVTDEVLRILESLSPLAPLHQPHNIAGILAAR--EAW 141 7765553....3466789999**********************************************9..888 PP TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216 +++++va+FDtafH+ p + ++alP+++y+e gvRrYGfHG+s++yvt++++++ + +++v+HlGn NCBI__GCF_000746085.1:WP_036261519.1 142 PHVRQVACFDTAFHRAHPFVNDVFALPRKFYDE-GVRRYGFHGLSYEYVTEKLQQVAPL-HAAGRVVVAHLGN 212 9999***********************999976.9******************999887.67889******** PP TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289 Gas++a+++G s+ smG+t L+Gl mGtR+G++Dp+++ yl+++ ++s+++i ++l ++sGl g+sg+s D+ NCBI__GCF_000746085.1:WP_036261519.1 213 GASMCAIRDGLSVASSMGFTALDGLPMGTRCGQLDPGVVLYLMQEMKMSAEAIADLLYRESGLKGLSGVSHDM 285 ************************************************************************* PP TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362 R++++ + ea+ A++ +v Ri++ +g +a leg lDa+vF gGiGe a vre+vle++e +G++ld NCBI__GCF_000746085.1:WP_036261519.1 286 RELEASD---RPEARQAIEYFVFRIRRELGGLAAVLEG-LDAMVFCGGIGEHAWRVRERVLEGMEWIGIELDR 354 **99877...7789**********************99.*********************************9 PP TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalr 402 n +e+vis++ s+v+v+vipt+ee +ia+ +l NCBI__GCF_000746085.1:WP_036261519.1 355 TANR----ASEQVISSQRSRVRVFVIPTDEEAMIARQTLA 390 9988....7899***********************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (400 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 28.43 // [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