Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_022530736.1 L248_RS13095 acetate kinase
Query= BRENDA::Q9F1X7 (397 letters) >NCBI__GCF_000469325.1:WP_022530736.1 Length = 396 Score = 438 bits (1126), Expect = e-127 Identities = 214/394 (54%), Positives = 292/394 (74%), Gaps = 1/394 (0%) Query: 3 KIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKNHE 62 KI+AVN GSSTLK+KLY+MP E+VLAEG+++R+ L S +K+ +G K ++ D+KN E Sbjct: 2 KILAVNTGSSTLKWKLYDMPAEHVLAEGMLDRMGLGDSVFTVKF-NGSKTKEVGDIKNAE 60 Query: 63 QAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAPLH 122 +A++ L+ L+D II + EI G+GHR+VAGGE F +S ++TP+ +KK+ L + APLH Sbjct: 61 EAVKKLMATLIDRKIIGSFDEIAGIGHRIVAGGETFTESALMTPENIKKVRGLADFAPLH 120 Query: 123 EPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHGIG 182 PA GI+AF K+LP++ V VFDTAFH T+P++N+LYS+P EYY KY ARKYG HG Sbjct: 121 NPAEAGGIEAFAKILPNVPQVGVFDTAFHTTMPKENYLYSIPMEYYRKYGARKYGAHGTS 180 Query: 183 NRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATRSG 242 +RYVS RAAELL + LKMI H+G+G S+ +K+GKS DTSMGFTP+ G+TM+TRSG Sbjct: 181 HRYVSARAAELLHADLKSLKMITLHMGSGVSVTAIKDGKSLDTSMGFTPLAGVTMSTRSG 240 Query: 243 DVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVARE 302 D+D SL+AY+M K +TD N+MI +LNTKSG+ GIS +S DMR++E T P++K+A + Sbjct: 241 DIDASLVAYLMGKLKITDPNQMIDILNTKSGIYGISELSPDMRQLEQTIDTRPQSKLAID 300 Query: 303 IYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDVRG 362 I+VNRII+Y+G+Y A MGG D +VFTAG+GE I +R + + LNY G +D E+NDV Sbjct: 301 IFVNRIIKYIGSYTAIMGGLDVLVFTAGIGEGDIKMRDRIVKKLNYMGAKIDPERNDVMA 360 Query: 363 VVRDISAKDSKIKTLLVPTDEELMIVRDVQTLAN 396 R IS DS +K +LVPT+EELMI RD +A+ Sbjct: 361 KERLISTDDSSVKVMLVPTNEELMIARDTVRVAH 394 Lambda K H 0.316 0.135 0.372 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: 478 Number of extensions: 20 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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_022530736.1 L248_RS13095 (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.811962.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-151 488.7 0.6 6.9e-151 488.5 0.6 1.0 1 NCBI__GCF_000469325.1:WP_022530736.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000469325.1:WP_022530736.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 488.5 0.6 6.9e-151 6.9e-151 4 404 .. 1 393 [. 1 394 [. 0.98 Alignments for each domain: == domain 1 score: 488.5 bits; conditional E-value: 6.9e-151 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 +kil +n+Gss lk++l+d+ +e+vl++g+ +r+ l ++ ++tv++++ k++e+ +i++ eeavkkl+ tl NCBI__GCF_000469325.1:WP_022530736.1 1 MKILAVNTGSSTLKWKLYDMP-AEHVLAEGMLDRMGLGDS-VFTVKFNGSKTKEVGDIKNAEEAVKKLMATLI 71 69*******************.7****************9.999***************************** PP TIGR00016 77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149 d+ki+ + +eia iGHR+v Gge+ftes+++t e +kk++ ++++APlHnpae+ giea+ k+l+++++v NCBI__GCF_000469325.1:WP_022530736.1 72 -DRKIIGSFDEIAGIGHRIVAGGETFTESALMTPENIKKVRGLADFAPLHNPAEAGGIEAFA--KILPNVPQV 141 .8************************************************************..99******* PP TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222 vFDtafH+t+p+e+ylY++P+++y+++g R+YG+HGtsh+yv+ raa+ll l++l++i++H+G G sv+a NCBI__GCF_000469325.1:WP_022530736.1 142 GVFDTAFHTTMPKENYLYSIPMEYYRKYGARKYGAHGTSHRYVSARAAELLHADLKSLKMITLHMGSGVSVTA 214 ************************************************************************* PP TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgls.ldeieetlnkksGllgisglssDlRdild 294 +k+Gks+dtsmG+tPL+G+ m tRsGdiD +++ yl+ +l+ + +++ ++ln ksG+ gis+ls D+R++++ NCBI__GCF_000469325.1:WP_022530736.1 215 IKDGKSLDTSMGFTPLAGVTMSTRSGDIDASLVAYLMGKLKITdPNQMIDILNTKSGIYGISELSPDMRQLEQ 287 ***************************************99884799************************** PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 + +++ ++klA++++v+Ri kyig+y+a + g lD +vFt+GiGe + ++r+++++kl+ +G k+d+e+n NCBI__GCF_000469325.1:WP_022530736.1 288 TI-DTRPQSKLAIDIFVNRIIKYIGSYTAIMGG-LDVLVFTAGIGEGDIKMRDRIVKKLNYMGAKIDPERND- 357 **.8999************************76.**************************************. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrla 404 + ke++ist++s+vkv+ +ptneel+ia+D++r+a NCBI__GCF_000469325.1:WP_022530736.1 358 -VMAKERLISTDDSSVKVMLVPTNEELMIARDTVRVA 393 .99*******************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (396 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: 24.32 // [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