Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate CA265_RS10080 CA265_RS10080 acetate kinase
Query= BRENDA::P38502 (408 letters) >FitnessBrowser__Pedo557:CA265_RS10080 Length = 398 Score = 383 bits (983), Expect = e-111 Identities = 199/398 (50%), Positives = 271/398 (68%), Gaps = 7/398 (1%) Query: 1 MKVLVINAGSSSLKYQLIDMTNESALAVGLCERIGIDNSIITQKKFDGKK---LEKLTDL 57 M +LVIN+GSSSLKYQL +M ++ L GL ERIGI+ S I + + +E+ + Sbjct: 1 MNILVINSGSSSLKYQLFNMPEKAPLCSGLVERIGIEGSFIKHSVYRNNEKYNIEQSGFI 60 Query: 58 PTHKDALEEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVEKAIKDCF 117 H + L++V+ LT+ E+ VI +I AVGHRVVHGGE FT + L + V+ IK F Sbjct: 61 ANHGEGLKQVLALLTEGEYAVIASPDDIAAVGHRVVHGGEHFTGATLITDEVKHQIKKLF 120 Query: 118 ELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYEKHGVRKY 177 LAPLHNP N I + + VFDTAFHQT+P AY YA+P Y++HG+R Y Sbjct: 121 SLAPLHNPVNYKCIEVAEQTFVNAKQIAVFDTAFHQTIPEQAYRYAIPEWYYKEHGIRVY 180 Query: 178 GFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGFTPLEGLA 237 GFHGTSHKYV+E+A L K E+KII+ HLGNG SITA++ GKS++TSMGF PL GL Sbjct: 181 GFHGTSHKYVSEQAIKWLNK--AESKIISIHLGNGCSITAIKNGKSIDTSMGFGPLSGLM 238 Query: 238 MGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGNRK 297 MGTR G IDP+++ LME G T ++ TL+NK+SG+LGV G S+D RD+ + S+GN Sbjct: 239 MGTRSGDIDPSVIFHLMEHSGYTLEQLSTLVNKQSGLLGVGG-SSDMRDIRKMVSEGNAA 297 Query: 298 AELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGIGIKIDDE 357 A LAL+++AY++KKFIG Y+A+LNG DA+VFTAG+GEN +++R+ + + LD +GI++D Sbjct: 298 AILALKLYAYRIKKFIGAYAAILNGIDAIVFTAGVGENDSNMREAVCSALDYLGIELDPN 357 Query: 358 KN-KIRGQEIDISTPDAKVRVFVIPTNEELAIARETKE 394 +N G +I+ AKV++ VIPTNEE IA + E Sbjct: 358 QNAAYHGALKEINKTGAKVKILVIPTNEEYEIAHQCFE 395 Lambda K H 0.316 0.135 0.380 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: 442 Number of extensions: 14 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: 408 Length of database: 398 Length adjustment: 31 Effective length of query: 377 Effective length of database: 367 Effective search space: 138359 Effective search space used: 138359 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 CA265_RS10080 CA265_RS10080 (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.8004.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-154 498.1 1.8 9.2e-154 497.9 1.8 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS10080 CA265_RS10080 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS10080 CA265_RS10080 acetate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 497.9 1.8 9.2e-154 9.2e-154 4 401 .. 1 394 [. 1 398 [] 0.95 Alignments for each domain: == domain 1 score: 497.9 bits; conditional E-value: 9.2e-154 TIGR00016 4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv..edgekke.eeklaiedheeav 68 + ilv+n+Gssslk++l+++ + + l+sglveri +e+++ik ++ek + e+ i++h e++ lcl|FitnessBrowser__Pedo557:CA265_RS10080 1 MNILVINSGSSSLKYQLFNMPE-KAPLCSGLVERIGIEGSFIKHSvyRNNEKYNiEQSGFIANHGEGL 67 579******************5.7779*************9997643444444413445579****** PP TIGR00016 69 kkllntlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegie 135 k++l l++ + +++ + ++ia++GHRvvhGge+ft ++++tdev ++ik++ +lAPlHnp + + ie lcl|FitnessBrowser__Pedo557:CA265_RS10080 68 KQVLALLTEgEYAVIASPDDIAAVGHRVVHGGEHFTGATLITDEVKHQIKKLFSLAPLHNPVNYKCIE 135 ********999********************************************************* PP TIGR00016 136 avlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkp 203 + ++ ++ak++avFDtafHqtipe+ay Ya+P+ +yke+g+R YGfHGtshkyv+++a k lnk lcl|FitnessBrowser__Pedo557:CA265_RS10080 136 VAE--QTFVNAKQIAVFDTAFHQTIPEQAYRYAIPEWYYKEHGIRVYGFHGTSHKYVSEQAIKWLNK- 200 ***..6778899*******************************************************. PP TIGR00016 204 lddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeiee 271 +++++i++HlGnG s++a+knGksidtsmG+ PL Gl+mGtRsGdiDp++i++l+e+ g +l+++ + lcl|FitnessBrowser__Pedo557:CA265_RS10080 201 -AESKIISIHLGNGCSITAIKNGKSIDTSMGFGPLSGLMMGTRSGDIDPSVIFHLMEHSGYTLEQLST 267 .999**************************************************************** PP TIGR00016 272 tlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiG 339 ++nk+sGllg+ g ssD+Rdi + ++egn a lAlk+y++Ri+k+ig+y+a l+g +DaivFt+G+G lcl|FitnessBrowser__Pedo557:CA265_RS10080 268 LVNKQSGLLGVGG-SSDMRDIRKMVSEGNAAAILALKLYAYRIKKFIGAYAAILNG-IDAIVFTAGVG 333 *************.****************************************88.*********** PP TIGR00016 340 enaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401 en++++re v+++l+ lG++ld+++n a +g + i+++ +kvk+lviptnee ia+ ++ lcl|FitnessBrowser__Pedo557:CA265_RS10080 334 ENDSNMREAVCSALDYLGIELDPNQNA-AYHGALKEINKTGAKVKILVIPTNEEYEIAHQCF 394 **************************9.8999999***********************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (405 nodes) Target sequences: 1 (398 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7.49 // [ok]
This GapMind analysis is from Sep 17 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