Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_008509973.1 BIBO1_RS16460 acetate/propionate family kinase
Query= curated2:Q6N143 (398 letters) >NCBI__GCF_000182725.1:WP_008509973.1 Length = 401 Score = 302 bits (773), Expect = 1e-86 Identities = 165/397 (41%), Positives = 247/397 (62%), Gaps = 13/397 (3%) Query: 1 MSDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDGSTRYDTY 60 M+ L+ NAGSS++K ++E + A + +G I G F++ +G+ D Sbjct: 1 MNKQLVTFNAGSSTVKIGVFEC--DGNAARKVSKGDIDLTGSPLRFRLRGENGNL--DIV 56 Query: 61 LPEGTSHDDAMAVLIGWIETTFPEH----RLSAVGHRVVHGGALFDGPVDVTPEVIAQLR 116 L S D + ++G + EH R+ AVGHRVV GG F V + + + + Sbjct: 57 L--SASGTDDITTILGELFDRLAEHIDPSRILAVGHRVVFGGDDFAQAVLIDDDNLEAIE 114 Query: 117 AFDRLAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVR 176 APLHQP +++ I+A+ K+ P L Q A FDTAFH +P+ FA+P+EL ++G++ Sbjct: 115 RLSIFAPLHQPKSLALIKAVRKIFPHLAQTASFDTAFHQTIPDTVRRFAIPQELHDRGIK 174 Query: 177 RYGFHGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDG 236 R+GFHGLSY+ I G A + +A+G+++ AHLG+GAS+CAM + +S+ T+M F+ LDG Sbjct: 175 RFGFHGLSYKSIIGNFSQRAPE-LAEGKIIAAHLGSGASLCAMHKRKSLDTSMSFSTLDG 233 Query: 237 LMMGSRCGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLASDDPHA 296 + M +RCG LDPGV+L+LL+++ M + + DLLY SGLLG+SG+S D R LL SD P A Sbjct: 234 IPMATRCGALDPGVLLHLLQQEKMESDALADLLYHRSGLLGLSGLSGDTRDLLESDAPQA 293 Query: 297 CEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDA 356 A+++F RIA E+ LA+ L GLDA++FT GIGEH IR +C++ AW GV LDP A Sbjct: 294 RAALDIFALRIAGEICRLASTLNGLDAVIFTAGIGEHQPAIRAAICQRLAWQGVELDPAA 353 Query: 357 NASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393 N A I++ S+ +A+ +PTDE+ +IA + + Sbjct: 354 ND--ENAFCITSRTSRTAAFVLPTDEEQIIASETFEI 388 Lambda K H 0.321 0.137 0.413 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: 421 Number of extensions: 15 Number of successful extensions: 3 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: 398 Length of database: 401 Length adjustment: 31 Effective length of query: 367 Effective length of database: 370 Effective search space: 135790 Effective search space used: 135790 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_008509973.1 BIBO1_RS16460 (acetate/propionate family 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.3317766.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-96 307.6 0.0 6.7e-96 307.4 0.0 1.0 1 NCBI__GCF_000182725.1:WP_008509973.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000182725.1:WP_008509973.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.4 0.0 6.7e-96 6.7e-96 4 403 .. 3 388 .. 1 390 [. 0.91 Alignments for each domain: == domain 1 score: 307.4 bits; conditional E-value: 6.7e-96 TIGR00016 4 kkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntl 75 k+++ naGss +k +++ + + +++ +g ++ + ++ + ge+++ +++ ++ + ++++l +l NCBI__GCF_000182725.1:WP_008509973.1 3 KQLVTFNAGSSTVKIGVFECDGnAARKVSKGDIDLTGSPLRF---RLRGENGNLDIVLSASGTDDITTILGEL 72 567789*************98635666789988887777664...4577777888888888888888888888 PP TIGR00016 76 kkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkakn 148 + + + + s i ++GHRvv Gg++f+++v+++d+ l++i+++s +APlH p l i+av k++ ++ + NCBI__GCF_000182725.1:WP_008509973.1 73 FDRLAEHIDPSRILAVGHRVVFGGDDFAQAVLIDDDNLEAIERLSIFAPLHQPKSLALIKAVRKIF--PHLAQ 143 876666778899***************************************************555..5556* PP TIGR00016 149 vavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvs 221 a FDtafHqtip+ +a+P++l ++ g++r+GfHG+s+k + + ++ l++ ++i +HlG Gas++ NCBI__GCF_000182725.1:WP_008509973.1 144 TASFDTAFHQTIPDTVRRFAIPQEL-HDRGIKRFGFHGLSYKSIIGNFSQRAPE-LAEGKIIAAHLGSGASLC 214 **********************665.689*************999988888766.899*************** PP TIGR00016 222 avknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdild 294 a+++ ks+dtsm + L+G+ m tR+G +Dp+++ +l +++++ d++ ++l +sGllg+sgls D Rd+l+ NCBI__GCF_000182725.1:WP_008509973.1 215 AMHKRKSLDTSMSFSTLDGIPMATRCGALDPGVLLHLLQQEKMESDALADLLYHRSGLLGLSGLSGDTRDLLE 287 ***********************************************************************99 PP TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367 +a+ Al++++ Ria i + +++l+g lDa++Ft+GiGe + +r+ ++++l+ G++ld++ n NCBI__GCF_000182725.1:WP_008509973.1 288 SD---APQARAALDIFALRIAGEICRLASTLNG-LDAVIFTAGIGEHQPAIRAAICQRLAWQGVELDPAAND- 355 87...6789**********************88.***********************************999. PP TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDalrl 403 ++ i+++ s++ ++v+pt+ee +ia +++++ NCBI__GCF_000182725.1:WP_008509973.1 356 ---ENAFCITSRTSRTAAFVLPTDEEQIIASETFEI 388 ...67778999*******************998766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (401 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: 18.58 // [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