Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_095512017.1 BSZ37_RS18750 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_002283365.1:WP_095512017.1 Length = 405 Score = 399 bits (1025), Expect = e-116 Identities = 211/398 (53%), Positives = 273/398 (68%), Gaps = 4/398 (1%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGDEK-HVIERELPDH 59 M VLV+N+GSSS+K LI+ + L G ERIG S RVGD K I + PDH Sbjct: 1 MTVLVLNAGSSSLKVDLIDAAAGQTLAAGQVERIGAVSSLASFRVGDAKPERISLKAPDH 60 Query: 60 EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119 AL +L T+ E G L +++AVGHRVVHGGERF ES L+D EV+ AI + LA Sbjct: 61 AAALSHLLETM-READGEEDRLPDVEAVGHRVVHGGERFAESALIDGEVVDAIRDAFDLA 119 Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179 PLHNPANL GI+AA K P VP VAVFDTAFHQTIP +AYLYA+P Y ++KIRRYGFH Sbjct: 120 PLHNPANLQGIRAAQKAFPDVPQVAVFDTAFHQTIPAEAYLYALPNRLYRRHKIRRYGFH 179 Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239 GTSH YVS+R E+ G + +++T H+GNG S+AA++ GK VDTSMG TPLEGLVMGT Sbjct: 180 GTSHYYVSRRLYELAGLDQQNSRVVTIHLGNGCSMAAIRDGKSVDTSMGMTPLEGLVMGT 239 Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299 RSGDLDP+I F +MEKE + E++ +LN+ SG+ GLS G+++DMRD+ A GD C+ Sbjct: 240 RSGDLDPSIVFEVMEKEDMPLAEVHTLLNRYSGLLGLS-GYAADMRDLLAEAADGDVRCQ 298 Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359 ++++ YR+ Y+G Y A + G+DA+ FTAG+G + R + L LG+ LD N Sbjct: 299 QAIDVFCYRVKSYLGRYLAVLGGLDAVAFTAGIGTFAAPVRAQILYGLAGLGMTLDAGAN 358 Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEI 397 E G E +I+TPDS V V VVPTNEEL+IA+DT+++ Sbjct: 359 -EAANGTEAVITTPDSAVPVWVVPTNEELVIAQDTQKL 395 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: 411 Number of extensions: 17 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 372 Effective length of database: 374 Effective search space: 139128 Effective search space used: 139128 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_095512017.1 BSZ37_RS18750 (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.593796.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-150 487.4 0.0 1.7e-150 487.2 0.0 1.0 1 NCBI__GCF_002283365.1:WP_095512017.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002283365.1:WP_095512017.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.2 0.0 1.7e-150 1.7e-150 5 403 .. 2 395 .. 1 397 [. 0.97 Alignments for each domain: == domain 1 score: 487.2 bits; conditional E-value: 1.7e-150 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 +lvlnaGssslk l+da+ ++l+ g veri + + + + k e++ l+ +dh++a+++ll+t+ + NCBI__GCF_002283365.1:WP_095512017.1 2 TVLVLNAGSSSLKVDLIDAAA-GQTLAAGQVERIGAVSSLASFRVGDAKPERISLKAPDHAAALSHLLETMRE 73 79******************6.5556*********999977777777789999*******************9 PP TIGR00016 78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150 + + l +++++GHRvvhGge+f+es++++ ev+++i+d+ +lAPlHnpa+l+gi+a++ k +++++va NCBI__GCF_002283365.1:WP_095512017.1 74 ADGEEDRLPDVEAVGHRVVHGGERFAESALIDGEVVDAIRDAFDLAPLHNPANLQGIRAAQ--KAFPDVPQVA 144 999999*******************************************************..7788999*** PP TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223 vFDtafHqtip eaylYalP +ly+++++RrYGfHGtsh+yv++r+ +l + ++++++++HlGnG s++a+ NCBI__GCF_002283365.1:WP_095512017.1 145 VFDTAFHQTIPAEAYLYALPNRLYRRHKIRRYGFHGTSHYYVSRRLYELAGLDQQNSRVVTIHLGNGCSMAAI 217 ************************************************************************* PP TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296 ++Gks+dtsmG+tPLeGlvmGtRsGd+Dp+i++ ++e++++ l+e++++ln+ sGllg+sg ++D+Rd+l++ NCBI__GCF_002283365.1:WP_095512017.1 218 RDGKSVDTSMGMTPLEGLVMGTRSGDLDPSIVFEVMEKEDMPLAEVHTLLNRYSGLLGLSGYAADMRDLLAEA 290 ************************************************************************* PP TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369 ++g+ +++ A++v+++R+++y+g+y+a l g lDa+ Ft+GiG aa vr+++l +l+ lG+ ld n+ a NCBI__GCF_002283365.1:WP_095512017.1 291 ADGDVRCQQAIDVFCYRVKSYLGRYLAVLGG-LDAVAFTAGIGTFAAPVRAQILYGLAGLGMTLDAGANE-AA 361 *****************************76.**************************************.88 PP TIGR00016 370 sgkesvisteeskvkvlviptneelviaeDalrl 403 +g+e+vi+t++s+v v v+ptneelvia+D+ +l NCBI__GCF_002283365.1:WP_095512017.1 362 NGTEAVITTPDSAVPVWVVPTNEELVIAQDTQKL 395 899****************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (405 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: 23.41 // [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