Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_040480655.1 C943_RS13315 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_000330725.2:WP_040480655.1 Length = 403 Score = 421 bits (1081), Expect = e-122 Identities = 215/407 (52%), Positives = 288/407 (70%), Gaps = 9/407 (2%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV----GDEKHVIEREL 56 M++LV+NSGSSS+KYQL E E LC G+ ERIG++GS + H+V G+ K I+R++ Sbjct: 1 MKILVLNSGSSSLKYQLFEFPNESPLCTGLVERIGLDGSIITHKVARDGGEAKFTIKRKI 60 Query: 57 PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116 +HEEAL + L+++ GV+ D+ E+ A+GHRVVHGGE+F + L+ +EV IEE+ Sbjct: 61 QNHEEALVTVTEILLEKDKGVLSDMSEVIAIGHRVVHGGEQFASTTLISDEVKDKIEELF 120 Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176 LAPLHNP NL+GI+ A ++ P VAVFDTAFHQT+P +AY +A+P E YEK IR Y Sbjct: 121 ALAPLHNPPNLLGIQVAERIFPQAKQVAVFDTAFHQTMPARAYRFAVPKEMYEKMGIRAY 180 Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236 GFHG+SH+YVSK A + L + +K+I+ H+GNG+SV A++ GK VD SMG P+ GLV Sbjct: 181 GFHGSSHQYVSKMAMKFL--QNPGVKLISIHLGNGSSVTAIEAGKSVDHSMGLGPMGGLV 238 Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296 MGTR GD+DP+I F ++ + GIS E+ DILNKKSG+ GL SDMRD+++A GD+ Sbjct: 239 MGTRCGDIDPSIIFHLINERGISAHELNDILNKKSGLLGLCG--HSDMRDVKDAIAAGDK 296 Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356 L E+Y YRI KYIG YAAAMNG+DAI+FTAG+GEN RE VC+ +EFLG++LD+ Sbjct: 297 DAALAYELYAYRIQKYIGMYAAAMNGLDAIIFTAGIGENDTDMREKVCANMEFLGIRLDQ 356 Query: 357 QKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEKIGR 403 N G I+ DS+VKV+VVPTNEEL I + T +V+ I R Sbjct: 357 SLNTARSSGIRE-INRSDSKVKVIVVPTNEELEIGQQTYHLVQAISR 402 Lambda K H 0.318 0.138 0.391 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: 455 Number of extensions: 19 Number of successful extensions: 5 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: 403 Length of database: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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_040480655.1 C943_RS13315 (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.67084.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-150 486.7 0.7 2.7e-150 486.5 0.7 1.0 1 NCBI__GCF_000330725.2:WP_040480655.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330725.2:WP_040480655.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 486.5 0.7 2.7e-150 2.7e-150 4 404 .. 1 397 [. 1 398 [. 0.96 Alignments for each domain: == domain 1 score: 486.5 bits; conditional E-value: 2.7e-150 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv...edgekkeeeklaiedheeavkklln 73 +kilvln+Gssslk++l++ n e+ l+ glveri l++++i+ + ge k ++k +i++heea+ ++ + NCBI__GCF_000330725.2:WP_040480655.1 1 MKILVLNSGSSSLKYQLFEFPN-ESPLCTGLVERIGLDGSIITHKvarDGGEAKFTIKRKIQNHEEALVTVTE 72 69*******************7.8889*************9987733233566778899************** PP TIGR00016 74 tlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145 l + dk +l ++se+ +iGHRvvhGge+f++++++ dev +ki+++ lAPlHnp++l gi+ + + ++ NCBI__GCF_000330725.2:WP_040480655.1 73 ILLEkDKGVLSDMSEVIAIGHRVVHGGEQFASTTLISDEVKDKIEELFALAPLHNPPNLLGIQVAE--RIFPQ 143 99887999*********************************************************9..78888 PP TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218 ak+vavFDtafHqt+p +ay +a+P+++y+++g+R YGfHG sh+yv++ a k l+ ++li++HlGnG+ NCBI__GCF_000330725.2:WP_040480655.1 144 AKQVAVFDTAFHQTMPARAYRFAVPKEMYEKMGIRAYGFHGSSHQYVSKMAMKFLQN--PGVKLISIHLGNGS 214 99*****************************************************99..689*********** PP TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291 sv+a++ Gks+d smGl P+ GlvmGtR+GdiDp+ii++l +++g s++e++++lnkksGllg+ g sD+Rd NCBI__GCF_000330725.2:WP_040480655.1 215 SVTAIEAGKSVDHSMGLGPMGGLVMGTRCGDIDPSIIFHLINERGISAHELNDILNKKSGLLGLCG-HSDMRD 286 ******************************************************************.99**** PP TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364 + d++++g+++a+lA+++y++Ri+kyig y+a+++g lDai+Ft+GiGen++++re+v+ ++e+lG++ld+ l NCBI__GCF_000330725.2:WP_040480655.1 287 VKDAIAAGDKDAALAYELYAYRIQKYIGMYAAAMNG-LDAIIFTAGIGENDTDMREKVCANMEFLGIRLDQSL 358 **********************************88.************************************ PP TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalrla 404 n+ ars + i+ ++skvkv+v+ptneel i + +++l+ NCBI__GCF_000330725.2:WP_040480655.1 359 NT-ARSSGIREINRSDSKVKVIVVPTNEELEIGQQTYHLV 397 *9.999999****************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (403 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.71 // [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