Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_097031061.1 CRO07_RS12690 acetate/propionate family kinase
Query= SwissProt::P37877 (395 letters) >NCBI__GCF_900207575.1:WP_097031061.1 Length = 396 Score = 257 bits (656), Expect = 5e-73 Identities = 152/384 (39%), Positives = 228/384 (59%), Gaps = 10/384 (2%) Query: 5 IAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDHAVAV 64 + +N GSS++KF LF++ + L +G VE IG+ + +G A + Sbjct: 6 LVLNIGSSTVKFGLFDIQDASPLVRGAVEGIGLRPRLKAHLPDGTLELRAPADARDAKEL 65 Query: 65 KMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPLHNPA 124 + L L E G + L ++ GHRVVHGG F+ VLLT E I+ +E LAP H P Sbjct: 66 TLWLLGLLE-GRLGPL-DLHAAGHRVVHGGPDFNAPVLLTPEVIERLEGFCPLAPGHQPF 123 Query: 125 NIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGTSHKY 184 N+ GI+A + P VP VA FDTAFH P + LY+LP + ++ GI +YGFHG S+ + Sbjct: 124 NLAGIRAVEARWPGVPQVACFDTAFHHDRPRIARLYALPRDLTDQ-GILRYGFHGLSYDF 182 Query: 185 VTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRSGNID 244 V R ++LG + R+I HLG+GAS+ A+ KS DT+MGF+ L G+ MGTR G ID Sbjct: 183 VASRLPDVLGAKARG-RVIVAHLGSGASLCALHDLKSTDTTMGFSALDGLMMGTRCGQID 241 Query: 245 PALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETALEVFA 304 P ++ +++ + G T E+ + L ++SGLLG+SG S D+RD++++ + A A+E+F Sbjct: 242 PGVLLHLL-RQGMTGPEIESLLGRQSGLLGVSGLSPDMRDLLDS---DHPEAAEAVELFV 297 Query: 305 SRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNVRGEEA 364 + + +G+ AA M G+DA++FTAGIG++S E+R RV+ L ++G+ DP N Sbjct: 298 RFVVRQVGALAAGMGGLDALVFTAGIGQHSPEIRARVMAALGWLGLDPDPEAN--AQSRT 355 Query: 365 FISYPHSPVKVMIIPTDEEVMIAR 388 +S S V +I TDEE +I R Sbjct: 356 ILSRAGSRVMAAVIATDEEAVILR 379 Lambda K H 0.317 0.136 0.381 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: 364 Number of extensions: 22 Number of successful extensions: 6 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: 395 Length of database: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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_097031061.1 CRO07_RS12690 (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.1088158.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-101 325.9 0.0 2e-101 325.6 0.0 1.0 1 NCBI__GCF_900207575.1:WP_097031061.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900207575.1:WP_097031061.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 325.6 0.0 2e-101 2e-101 5 398 .. 4 379 .. 1 384 [. 0.93 Alignments for each domain: == domain 1 score: 325.6 bits; conditional E-value: 2e-101 TIGR00016 5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkk 77 + lvln Gss +kf l+d ++++ + ++g ve i l + dg + ++ + +d +e ll l+ NCBI__GCF_900207575.1:WP_097031061.1 4 VWLVLNIGSSTVKFGLFDIQDASPL-VRGAVEGIGLRPRLKAHLPDGTLELRAPADARDAKELTLWLLGLLEG 75 679*****************86655.************98888888888888888888877766666666664 PP TIGR00016 78 dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknva 150 + ++++ GHRvvhGg +f+ v++t ev+++++ + +lAP H p +l gi+av + +++va NCBI__GCF_900207575.1:WP_097031061.1 76 ----RLGPLDLHAAGHRVVHGGPDFNAPVLLTPEVIERLEGFCPLAPGHQPFNLAGIRAVE--ARWPGVPQVA 142 ....44566899*************************************************..889999**** PP TIGR00016 151 vFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsav 223 +FDtafH+ p+ a lYalP++l +++g+ rYGfHG+s+ +v+ r+ ++l+ + ++iv+HlG Gas++a+ NCBI__GCF_900207575.1:WP_097031061.1 143 CFDTAFHHDRPRIARLYALPRDL-TDQGILRYGFHGLSYDFVASRLPDVLGA-KARGRVIVAHLGSGASLCAL 213 ********************776.678************************9.57789*************** PP TIGR00016 224 knGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkk 296 ++ ks dt+mG+ L+Gl+mGtR+G+iDp+++ +l +g++ eie++l ++sGllg+sgls D+Rd+ld NCBI__GCF_900207575.1:WP_097031061.1 214 HDLKSTDTTMGFSALDGLMMGTRCGQIDPGVLLHLLR-QGMTGPEIESLLGRQSGLLGVSGLSPDMRDLLDSD 285 **********************************986.79******************************998 PP TIGR00016 297 eegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaar 369 + ea+ A++++v + + +g+ +a + g lDa+vFt+GiG+ + e+r++v+ +l lGl+ d+e n NCBI__GCF_900207575.1:WP_097031061.1 286 ---HPEAAEAVELFVRFVVRQVGALAAGMGG-LDALVFTAGIGQHSPEIRARVMAALGWLGLDPDPEANA--- 351 ...78899*********************76.************************************99... PP TIGR00016 370 sgkesvisteeskvkvlviptneelviae 398 ++ +++s s+v ++vi t+ee vi++ NCBI__GCF_900207575.1:WP_097031061.1 352 -QSRTILSRAGSRVMAAVIATDEEAVILR 379 .778999********************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (396 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: 00:00:00.01 # Mc/sec: 13.89 // [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