Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011371692.1 SUDEN_RS00280 acetate kinase
Query= BRENDA::G4T0C7 (401 letters) >NCBI__GCF_000012965.1:WP_011371692.1 Length = 389 Score = 346 bits (887), Expect = e-100 Identities = 189/395 (47%), Positives = 253/395 (64%), Gaps = 16/395 (4%) Query: 8 ILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQSVIAAD 67 I VINSGSSSIK++L +PQ VLA +E+IGE S+I R D + K Sbjct: 3 IAVINSGSSSIKFKLYLMPQSIVLAHVHVEKIGETSSKITFRHTDKKEVFSNKIDT---- 58 Query: 68 HHQAFKAVFEILGEN------CSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIAP 121 HH+ + + +IL E S+DAI HRVVHGGD F L+++D I +R L ++P Sbjct: 59 HHEGLRVINDILKEYQIIEHFSSLDAIAHRVVHGGDFFKSATLINEDVIYKIRELIPLSP 118 Query: 122 LHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFHG 181 LHN NL GI L P VPQ+AVFDT+FH ++P AY YA+P Y ++ IRRFGFHG Sbjct: 119 LHNRANLEGILVSLKKAPSVPQIAVFDTSFHASLPKEAYLYALPYELYKEHKIRRFGFHG 178 Query: 182 TSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGTR 241 SH YV ++ A+ + K ++ITLHLGNG+SA AI NG+SVDTSMGFTPLEGLVMG+R Sbjct: 179 ISHAYVLKKVAQEMQKNLHGLNMITLHLGNGSSACAIRNGKSVDTSMGFTPLEGLVMGSR 238 Query: 242 SGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLAL 301 SGD+DP I +++++ D ++ LNR SGL G+CG DLR ++++ DE + +AL Sbjct: 239 SGDIDPQIVIYLQKELGYGLDEVEELLNRHSGLIGVCGEIDLREIIKR---DDELSHVAL 295 Query: 302 DLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSDV 361 D+ R+KKYIGAY A+LG VDA+ F G+GEN++EVR + L GI +D AN Sbjct: 296 DMMTRRVKKYIGAYMALLGRVDAIAFCAGIGENSSEVREKILKNLELFGIELDTKANEK- 354 Query: 362 TGAIAEIGLAESRTRILVIKTDEELQIAREAMAVL 396 + +I S+ + VI TDEEL+IA EA A+L Sbjct: 355 --NLTKISKQTSKIEVFVINTDEELEIALEAEALL 387 Lambda K H 0.320 0.137 0.400 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: 401 Number of extensions: 16 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: 401 Length of database: 389 Length adjustment: 31 Effective length of query: 370 Effective length of database: 358 Effective search space: 132460 Effective search space used: 132460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_011371692.1 SUDEN_RS00280 (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.19750.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-141 455.2 3.6 9.6e-141 455.1 3.6 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011371692.1 SUDEN_RS00280 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011371692.1 SUDEN_RS00280 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.1 3.6 9.6e-141 9.6e-141 4 401 .. 1 384 [. 1 388 [. 0.96 Alignments for each domain: == domain 1 score: 455.1 bits; conditional E-value: 9.6e-141 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkll 72 +ki v+n+Gsss+kf+l+ + + + vl++ ve+i ++i+ +++kke + +i+ h+e+++ + lcl|NCBI__GCF_000012965.1:WP_011371692.1 1 MKIAVINSGSSSIKFKLYLMPQ-SIVLAHVHVEKIGETSSKIT-FRHTDKKEVFSNKIDTHHEGLRVIN 67 6899****************95.78899*******99999665.677789****************999 PP TIGR00016 73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklk 141 + lk + +i+++ s++++i HRvvhGg+ f+++++++++v+ ki+++++l PlHn+a+legi l k lcl|NCBI__GCF_000012965.1:WP_011371692.1 68 DILK-EYQIIEHFSSLDAIAHRVVHGGDFFKSATLINEDVIYKIRELIPLSPLHNRANLEGILVSL--K 133 9998.799******************************************************8877..9 PP TIGR00016 142 vllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210 + ++++++avFDt+fH +p+eaylYalPy+lyke+++Rr+GfHG+sh yv +++a+ ++k+l+ ln+i lcl|NCBI__GCF_000012965.1:WP_011371692.1 134 KAPSVPQIAVFDTSFHASLPKEAYLYALPYELYKEHKIRRFGFHGISHAYVLKKVAQEMQKNLHGLNMI 202 99******************************************************************* PP TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGl 279 ++HlGnG+s +a++nGks+dtsmG+tPLeGlvmG+RsGdiDp i+ yl+++lg lde+ee+ln++sGl lcl|NCBI__GCF_000012965.1:WP_011371692.1 203 TLHLGNGSSACAIRNGKSVDTSMGFTPLEGLVMGSRSGDIDPQIVIYLQKELGYGLDEVEELLNRHSGL 271 ********************************************************************* PP TIGR00016 280 lgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrel 348 +g+ g DlR+i+++ +e +++Al++++ R++kyig+y+a l g++Dai F +GiGen++evre+ lcl|NCBI__GCF_000012965.1:WP_011371692.1 272 IGVCG-EIDLREIIKRDDEL---SHVALDMMTRRVKKYIGAYMALL-GRVDAIAFCAGIGENSSEVREK 335 *****.99******999555...59*********************.77******************** PP TIGR00016 349 vleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401 +l++le++G++ld++ n+ ++ + is++ sk++v+vi+t+eel ia +a lcl|NCBI__GCF_000012965.1:WP_011371692.1 336 ILKNLELFGIELDTKANE----KNLTKISKQTSKIEVFVINTDEELEIALEAE 384 ****************99....66788*********************98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (389 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 8.46 // [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