Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_035745643.1 CRO07_RS16695 acetate/propionate family kinase
Query= SwissProt::P11868 (402 letters) >NCBI__GCF_900207575.1:WP_035745643.1 Length = 389 Score = 242 bits (617), Expect = 2e-68 Identities = 155/391 (39%), Positives = 226/391 (57%), Gaps = 18/391 (4%) Query: 6 VVLVINCGSSSIK--FSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSYEGA 63 ++L N GSS+IK F L+A+ L SG+ D + G+ + G Sbjct: 5 LILTFNTGSSTIKLGFYALEAAAPRPLASGVIDFRDEPFEVRLTREGKTFSGPITADPGD 64 Query: 64 LKAI---AFELEKRNLNDS-VALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHN 119 L A+ AF + N S +A+IGHR+ HGG +FT A ITD+VI I ++ LAPLH Sbjct: 65 LTAVLNQAFAWLAGHFNLSRLAVIGHRVVHGGDVFTGPARITDQVIAQIDALARLAPLHQ 124 Query: 120 YANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSH 179 +L+ I + + L+P V Q A FDT+FH T P + LP Y++ G++RYGFHG S+ Sbjct: 125 PQSLALIRAMRGLYPDVPQTASFDTAFHATNPPLIRRFALPRALYDQ-GIKRYGFHGLSY 183 Query: 180 RYVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGD 239 RY++ + L D+ +V AHLG+GAS+CA+R G+S+D+SMG + L+G+ M TRSG Sbjct: 184 RYIAGQLGDLAT----DAKVVAAHLGSGASLCAIRGGKSIDSSMGFSTLDGIPMATRSGA 239 Query: 240 VDFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKT 299 +D G + + + QSL +E ++ +ESGLLG+SG +D R L + A AI Sbjct: 240 LDPGVILHLMGEMGQSLKQVETMLYRESGLLGVSGFEADSRELMAS---TRPEAAEAIDL 296 Query: 300 FVHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNS 359 F RIA +A A S+ +D ++FT GIGE+ IR V LA LG E+D + +N Sbjct: 297 FCLRIAGEVARLATSMGGIDALVFTAGIGEHQPGIRARVAARLAWLGAELDPD----ANE 352 Query: 360 CGERIVSSENARVICAVIPTNEEKMIALDAI 390 G R +S+ +RV VIPT+EE +IA +A+ Sbjct: 353 AGSRRISTAASRVQLLVIPTDEESIIAQEAV 383 Lambda K H 0.318 0.134 0.386 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: 346 Number of extensions: 13 Number of successful extensions: 5 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: 402 Length of database: 389 Length adjustment: 31 Effective length of query: 371 Effective length of database: 358 Effective search space: 132818 Effective search space used: 132818 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_035745643.1 CRO07_RS16695 (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.1343611.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-100 322.3 0.0 2.4e-100 322.0 0.0 1.0 1 NCBI__GCF_900207575.1:WP_035745643.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900207575.1:WP_035745643.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 322.0 0.0 2.4e-100 2.4e-100 3 401 .. 3 383 .. 1 386 [. 0.89 Alignments for each domain: == domain 1 score: 322.0 bits; conditional E-value: 2.4e-100 TIGR00016 3 skkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 +il n+Gss +k + e + + l+sg+++ + v + +++++ i++ ++++ln+ NCBI__GCF_900207575.1:WP_035745643.1 3 RDLILTFNTGSSTIKLGFYALEAaAPRPLASGVIDFRDEPFE----VRLTREGKTFSGPITADPGDLTAVLNQ 71 6789***********99998886244559*****96554444....333334445555555555555555555 PP TIGR00016 75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147 + + + +ls +a+iGHRvvhGg+ ft + +td+v+++i +++lAPlH p+ l i+a+ ++++ NCBI__GCF_900207575.1:WP_035745643.1 72 AFAWLAGHFNLSRLAVIGHRVVHGGDVFTGPARITDQVIAQIDALARLAPLHQPQSLALIRAMR--GLYPDVP 142 55544457899*****************************************************..889999* PP TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220 + a FDtafH t p +alP+ ly+ +g++rYGfHG+s++y++ + l+ + d +++ +HlG Gas+ NCBI__GCF_900207575.1:WP_035745643.1 143 QTASFDTAFHATNPPLIRRFALPRALYD-QGIKRYGFHGLSYRYIAGQ----LGDLATDAKVVAAHLGSGASL 210 ***********************88885.7***************876....5666789************** PP TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293 +a++ Gksid smG+ L+G+ m tRsG +Dp++i +l+ + g+sl+++e++l ++sGllg+sg+ +D R+++ NCBI__GCF_900207575.1:WP_035745643.1 211 CAIRGGKSIDSSMGFSTLDGIPMATRSGALDPGVILHLMGEMGQSLKQVETMLYRESGLLGVSGFEADSRELM 283 ************************************************************************9 PP TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366 + + + ea+ A+++++ Ria +++ ++s+ g +Da+vFt+GiGe + +r++v +l+ lG +ld++ n+ NCBI__GCF_900207575.1:WP_035745643.1 284 AST---RPEAAEAIDLFCLRIAGEVARLATSMGG-IDALVFTAGIGEHQPGIRARVAARLAWLGAELDPDANE 352 988...77899*********************76.*************************************9 PP TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDal 401 ++ ist s+v++lvipt+ee++ia++a+ NCBI__GCF_900207575.1:WP_035745643.1 353 ----AGSRRISTAASRVQLLVIPTDEESIIAQEAV 383 ....78899***********************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 20.29 // [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