Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate AZOBR_RS04605 AZOBR_RS04605 acetate kinase
Query= BRENDA::Q9WYB1 (403 letters) >FitnessBrowser__azobra:AZOBR_RS04605 Length = 398 Score = 261 bits (666), Expect = 3e-74 Identities = 164/405 (40%), Positives = 232/405 (57%), Gaps = 22/405 (5%) Query: 3 VLVINSGSSSIKYQLIEMEGEK--VLCKGIAERIGIEGSRLVHRVGDEKH-----VIERE 55 +LVIN+GSSSIK+QL + V +G E IG +V G + + E Sbjct: 5 ILVINAGSSSIKFQLFDAADGTLPVRLRGRIEGIGTAPRLIVQESGQDGSRDGGVTLPAE 64 Query: 56 LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115 D L + +LG + AVGHRVVHGG + V VD+ V+ +E Sbjct: 65 SGDGVPGALAFLGAWLRGRLGGAMPV----AVGHRVVHGGPAYDSHVAVDDAVIGTLETY 120 Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175 PLAPLH P NL I+A KLLP V VA FDTAFH+ + A YAIP + + +RR Sbjct: 121 VPLAPLHQPNNLAPIRAIRKLLPDVLQVACFDTAFHRHHSEPADRYAIP-DALHREGVRR 179 Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235 YGFHG S+ Y++ R + L + +++ H+G+GAS+ A++ G+ VD++MGFT L+GL Sbjct: 180 YGFHGLSYEYIAGRLPD-LAPGIAGGRVVVAHLGSGASMCAIQDGRSVDSTMGFTALDGL 238 Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295 MGTR G LDP + ++M+K G+ + + +L G+ GLS G S+D+RD+ + D Sbjct: 239 PMGTRPGQLDPGVVLYLMDK-GMDARAIERLLYHDCGLKGLS-GISNDVRDLLAST---D 293 Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355 KL L+ + YR + IGA AAAM G+D +VFTAG+GE +P R+ + +LGV LD Sbjct: 294 PRAKLALDCFVYRASLAIGALAAAMGGIDGLVFTAGIGERAPAIRKAIAERARWLGVDLD 353 Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400 + N I+TPDSRVK V+PT+EE MIA T+ I+ + Sbjct: 354 EAGNAANAL----CITTPDSRVKGWVIPTDEERMIALHTRAILRR 394 Lambda K H 0.318 0.138 0.391 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: 401 Number of extensions: 16 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: 403 Length of database: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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 AZOBR_RS04605 AZOBR_RS04605 (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.13848.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-102 326.6 0.0 2e-101 325.6 0.0 1.4 1 lcl|FitnessBrowser__azobra:AZOBR_RS04605 AZOBR_RS04605 acetate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS04605 AZOBR_RS04605 acetate kinase # 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 4 399 .. 3 387 .. 1 392 [. 0.88 Alignments for each domain: == domain 1 score: 325.6 bits; conditional E-value: 2e-101 TIGR00016 4 kkilvlnaGssslkfalldaense.kvllsglverikleeariktvedgekkeee..klaiedheeavk 69 + ilv+naGsss+kf+l+da+++ v l+g +e i + i e+g++++++ ++ ++ +v lcl|FitnessBrowser__azobra:AZOBR_RS04605 3 ETILVINAGSSSIKFQLFDAADGTlPVRLRGRIEGIGTAPRLIV-QESGQDGSRDggVTLPAESGDGVP 70 689******************965145699******99988555.455554444411222344445666 PP TIGR00016 70 kllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138 l l + + + + ++GHRvvhGg + + v v+d v+ ++ ++lAPlH p++l i+a+ lcl|FitnessBrowser__azobra:AZOBR_RS04605 71 GALAFLGAWLRGRLGGAMPVAVGHRVVHGGPAYDSHVAVDDAVIGTLETYVPLAPLHQPNNLAPIRAIR 139 666666653333444455578************************************************ PP TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddl 207 k l+++ +va+FDtafH+ e+a Ya+P ++ ++ gvRrYGfHG+s++y++ r+ +l ++ lcl|FitnessBrowser__azobra:AZOBR_RS04605 140 --KLLPDVLQVACFDTAFHRHHSEPADRYAIP-DALHREGVRRYGFHGLSYEYIAGRLPDLAP-GIAGG 204 ..8889999***********************.777788******************998655.59*** PP TIGR00016 208 nlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkk 276 +++v+HlG Gas++a+++G+s+d +mG+t L+Gl mGtR G++Dp+++ yl+++ g+ + +ie++l + lcl|FitnessBrowser__azobra:AZOBR_RS04605 205 RVVVAHLGSGASMCAIQDGRSVDSTMGFTALDGLPMGTRPGQLDPGVVLYLMDK-GMDARAIERLLYHD 272 ***************************************************985.999*********** PP TIGR00016 277 sGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaev 345 Gl g+sg+s+D+Rd+l+ + + +aklAl+ +v+R ig+ +a++ g +D++vFt+GiGe a + lcl|FitnessBrowser__azobra:AZOBR_RS04605 273 CGLKGLSGISNDVRDLLAST---DPRAKLALDCFVYRASLAIGALAAAMGG-IDGLVFTAGIGERAPAI 337 *****************998...789***********************76.***************** PP TIGR00016 346 relvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeD 399 r+ + e+ + lG++ld++ n + i+t++s+vk vipt+ee +ia lcl|FitnessBrowser__azobra:AZOBR_RS04605 338 RKAIAERARWLGVDLDEAGNA----ANALCITTPDSRVKGWVIPTDEERMIALH 387 ****************99998....67789*********************965 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 4.20 // [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