Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_012969836.1 ALVIN_RS03025 acetate kinase
Query= BRENDA::G4T0C7 (401 letters) >NCBI__GCF_000025485.1:WP_012969836.1 Length = 404 Score = 436 bits (1121), Expect = e-127 Identities = 227/394 (57%), Positives = 283/394 (71%), Gaps = 8/394 (2%) Query: 8 ILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIKQ-SVIAA 66 +LV+NSGSSSIKY+L + Q LA GL+ RIGE E + DS ++ Q S+ + Sbjct: 3 VLVLNSGSSSIKYQLFRVQDWQALASGLVARIGEPEGEVKLNWLDSDEVSHSSQESLPIS 62 Query: 67 DHHQAFKAVFE------ILGENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIA 120 H Q + +L E + AIGHRVVHGG RF PA +DD I ++R + +A Sbjct: 63 SHEQGIDYIIRALRDSGVLVEVGELAAIGHRVVHGGVRFKQPARIDDSVIEAIREVVPLA 122 Query: 121 PLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFH 180 PLHNP +L GIE+ +HFPGVP VAVFDTAFHQTMPP AYRYAIPE Y+++ IRR+GFH Sbjct: 123 PLHNPGHLAGIEAACSHFPGVPSVAVFDTAFHQTMPPAAYRYAIPEALYTEHRIRRYGFH 182 Query: 181 GTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGT 240 GTSHHYVA+RAAE +GKP D+ +LI+LHLGNGASATAI G+ VDTSMG TPLEGLVMGT Sbjct: 183 GTSHHYVAKRAAELLGKPLDQCNLISLHLGNGASATAIRAGQCVDTSMGLTPLEGLVMGT 242 Query: 241 RSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLA 300 RSGD+DPA+ +++ + D D +DR LNR+SGL GLCG ND+R + + AGDERA LA Sbjct: 243 RSGDIDPAVVIYLCKHLGLDADGLDRLLNRQSGLLGLCGVNDMREIDQLAAAGDERAELA 302 Query: 301 LDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAAN-S 359 + + +R+KKYIGAYYA LG VDALVFTGG+GENAAE+RR ACEGL RLGI +D N S Sbjct: 303 IAITTHRLKKYIGAYYAELGRVDALVFTGGIGENAAEIRRRACEGLERLGIRLDTELNAS 362 Query: 360 DVTGAIAEIGLAESRTRILVIKTDEELQIAREAM 393 I L ES R+LV+ T+EEL+IA++A+ Sbjct: 363 RAQRGERCISLPESEVRVLVVPTNEELEIAQQAL 396 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: 513 Number of extensions: 14 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: 401 Length of database: 404 Length adjustment: 31 Effective length of query: 370 Effective length of database: 373 Effective search space: 138010 Effective search space used: 138010 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_012969836.1 ALVIN_RS03025 (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.10251.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-153 494.9 0.0 8.8e-153 494.7 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012969836.1 ALVIN_RS03025 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012969836.1 ALVIN_RS03025 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 494.7 0.0 8.8e-153 8.8e-153 4 403 .. 1 398 [. 1 400 [. 0.95 Alignments for each domain: == domain 1 score: 494.7 bits; conditional E-value: 8.8e-153 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleearik..tv..edgekkeeeklaiedheeav 68 +k+lvln+Gsss+k++l+ ++ + l+sglv ri +e +k ++ + ++ ++e l i++he+++ lcl|NCBI__GCF_000025485.1:WP_012969836.1 1 MKVLVLNSGSSSIKYQLFRVQD-WQALASGLVARIGEPEGEVKlnWLdsDEVSHSSQESLPISSHEQGI 68 69*******************8.6677*********99876651144222334567788899******* PP TIGR00016 69 kkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieav 137 + ++++l d+ +l e e+a+iGHRvvhGg +f++ + ++d+v+++i+++++lAPlHnp +l giea+ lcl|NCBI__GCF_000025485.1:WP_012969836.1 69 DYIIRALR-DSGVLVEVGELAAIGHRVVHGGVRFKQPARIDDSVIEAIREVVPLAPLHNPGHLAGIEAA 136 ********.8*********************************************************** PP TIGR00016 138 lklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206 + ++ vavFDtafHqt+p ay Ya+P+ ly+e+ +RrYGfHGtsh+yv++raa+ll+kpld+ lcl|NCBI__GCF_000025485.1:WP_012969836.1 137 C--SHFPGVPSVAVFDTAFHQTMPPAAYRYAIPEALYTEHRIRRYGFHGTSHHYVAKRAAELLGKPLDQ 203 *..7888899*********************************************************** PP TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnk 275 nli++HlGnGas +a++ G+++dtsmGltPLeGlvmGtRsGdiDpa++ yl ++lgl +d + ++ln+ lcl|NCBI__GCF_000025485.1:WP_012969836.1 204 CNLISLHLGNGASATAIRAGQCVDTSMGLTPLEGLVMGTRSGDIDPAVVIYLCKHLGLDADGLDRLLNR 272 ********************************************************************* PP TIGR00016 276 ksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaae 344 +sGllg+ g +D+R+i + ++g+e+a+lA+ + +hR++kyig+y a+l g++Da+vFtgGiGenaae lcl|NCBI__GCF_000025485.1:WP_012969836.1 273 QSGLLGLCG-VNDMREIDQLAAAGDERAELAIAITTHRLKKYIGAYYAEL-GRVDALVFTGGIGENAAE 339 *********.89**************************************.67**************** PP TIGR00016 345 vrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403 +r++++e+le lG++ld+eln + e+ is +es+v+vlv+ptneel ia+ alr lcl|NCBI__GCF_000025485.1:WP_012969836.1 340 IRRRACEGLERLGIRLDTELNASRAQRGERCISLPESEVRVLVVPTNEELEIAQQALRT 398 **********************889999**************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.06 // [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