Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_092344577.1 BLU87_RS03090 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >NCBI__GCF_900107645.1:WP_092344577.1 Length = 421 Score = 422 bits (1086), Expect = e-123 Identities = 216/401 (53%), Positives = 284/401 (70%), Gaps = 3/401 (0%) Query: 1 MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-GDEKHVIERELPDH 59 M +L +N GSSS+KYQL + ++V+ KG+ ER+ I S ++H V G + + E E PDH Sbjct: 1 MDILALNCGSSSVKYQLFDWAKKEVIAKGMVERVTIGDSYIIHEVSGRDTYHEEYECPDH 60 Query: 60 EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119 + A+ LI+ L D+ GV++D+ I AVGHRVVHGGE+F +SV +D VL AI+EV LA Sbjct: 61 KTAVHLIVKILTDKTHGVLEDITSISAVGHRVVHGGEKFTKSVRIDATVLDAIKEVQHLA 120 Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179 PLHNP N+ GI+AA LP VP++A+FDTAFHQ++P+ AY Y +P+++Y+ Y +RRYGFH Sbjct: 121 PLHNPPNIAGIEAAQANLPDVPHIAIFDTAFHQSMPEYAYTYPVPHQWYQDYGVRRYGFH 180 Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239 GTSH YVSKRAA +L K ++ +IT HIGNG S A+K G +DTSMG TPLEG VMGT Sbjct: 181 GTSHLYVSKRAAALLEKDPQDCNLITMHIGNGVSHTAIKNGLSIDTSMGLTPLEGAVMGT 240 Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299 R GD+DPAIP FIME+E +SP E+ ILNKKSG+ G++ F D RD+ EAA G+E C Sbjct: 241 RCGDIDPAIPAFIMEREHLSPHEIDSILNKKSGILGITGEF-IDRRDVIEAAEAGNERCV 299 Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359 L L I YR+ KYIG+Y A + +DA+VFTAGVGE + RE LE +G+KLDK KN Sbjct: 300 LALAIEGYRLKKYIGSYCAVLGRLDAVVFTAGVGEMGWLIREKALEDLEHIGIKLDKDKN 359 Query: 360 EETI-RGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVE 399 T+ R +E I+T DS VKV V+PT+EEL+ D I+E Sbjct: 360 RRTMTRKRETTITTDDSPVKVFVIPTDEELVFTEDVVAIME 400 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: 483 Number of extensions: 14 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: 421 Length adjustment: 31 Effective length of query: 372 Effective length of database: 390 Effective search space: 145080 Effective search space used: 145080 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_092344577.1 BLU87_RS03090 (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.19859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-154 498.1 0.0 9.6e-154 497.9 0.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344577.1 BLU87_RS03090 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344577.1 BLU87_RS03090 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 497.9 0.0 9.6e-154 9.6e-154 5 403 .. 2 398 .. 1 400 [. 0.98 Alignments for each domain: == domain 1 score: 497.9 bits; conditional E-value: 9.6e-154 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 il ln+Gsss+k++l+d ++ ++v+++g+ver+++ ++ i ++g ++ +e+ + +dh++av+ +++ lcl|NCBI__GCF_900107645.1:WP_092344577.1 2 DILALNCGSSSVKYQLFDWAK-KEVIAKGMVERVTIGDSYIIHEVSGRDTYHEEYECPDHKTAVHLIVK 69 69******************5.8899******************************************* PP TIGR00016 74 tlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklk 141 l++ + +l++ +i+++GHRvvhGgekft+sv +++ vl++ik++ +lAPlHnp+++ giea++ lcl|NCBI__GCF_900107645.1:WP_092344577.1 70 ILTDkTHGVLEDITSISAVGHRVVHGGEKFTKSVRIDATVLDAIKEVQHLAPLHNPPNIAGIEAAQ--A 136 ***97899**********************************************************..9 PP TIGR00016 142 vllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210 l++++++a+FDtafHq +pe ay Y++P+++y+++gvRrYGfHGtsh yv++raa ll+k +d nli lcl|NCBI__GCF_900107645.1:WP_092344577.1 137 NLPDVPHIAIFDTAFHQSMPEYAYTYPVPHQWYQDYGVRRYGFHGTSHLYVSKRAAALLEKDPQDCNLI 205 99******************************************************************* PP TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGl 279 ++H+GnG s +a+knG sidtsmGltPLeG vmGtR+GdiDpai +++e++ ls +ei ++lnkksG+ lcl|NCBI__GCF_900107645.1:WP_092344577.1 206 TMHIGNGVSHTAIKNGLSIDTSMGLTPLEGAVMGTRCGDIDPAIPAFIMEREHLSPHEIDSILNKKSGI 274 ********************************************************************* PP TIGR00016 280 lgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrel 348 lgi+g D Rd++++ e+gne++ lAl + +R++kyig+y a l g+lDa+vFt+G+Ge +re+ lcl|NCBI__GCF_900107645.1:WP_092344577.1 275 LGITGEFIDRRDVIEAAEAGNERCVLALAIEGYRLKKYIGSYCAVL-GRLDAVVFTAGVGEMGWLIREK 342 **********************************************.67******************** PP TIGR00016 349 vleklevlGlkldlelnnaa.rsgkesvisteeskvkvlviptneelviaeDalrl 403 +le+le +G+kld+++n ++ ++++e+ i+t++s vkv+vipt+eelv eD++ + lcl|NCBI__GCF_900107645.1:WP_092344577.1 343 ALEDLEHIGIKLDKDKNRRTmTRKRETTITTDDSPVKVFVIPTDEELVFTEDVVAI 398 ******************9978899***************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (421 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: 00:00:00.01 # Mc/sec: 10.88 // [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