Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate GFF836 Psest_0850 glucokinase, proteobacterial type
Query= reanno::WCS417:GFF4431 (318 letters) >FitnessBrowser__psRCH2:GFF836 Length = 319 Score = 412 bits (1058), Expect = e-120 Identities = 201/318 (63%), Positives = 238/318 (74%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 M+LALVGDIGGTNARFALWRD L S+RV A AD ++PE A++ YL GL G + A C Sbjct: 1 MRLALVGDIGGTNARFALWRDSRLESVRVLAAADFATPEMAVEYYLASLGLAPGSVEAAC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 L+ AGPV G++F FTNNHWRL+++ FC LQ+ ELLL+NDF+AMALGMTR+ R++C Sbjct: 61 LACAGPVKGEQFTFTNNHWRLTRSDFCGALQMGELLLINDFAAMALGMTRVGEAGRRMIC 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 G EP PA+VIGPGTGLGV LL LG G + ALPGEGGHVDLP++ E LWQ ++ Sbjct: 121 AGEAEPDAPALVIGPGTGLGVAGLLPLGGGSWRALPGEGGHVDLPVADAHEAALWQMLFA 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 ++GHV AE LSGGGL LYR +C V G P L +P +TAA LAGD VA+ L+QF +W Sbjct: 181 QLGHVRAEDVLSGGGLLLLYRTVCTVAGLAPRLASPAEVTAAALAGDHVAVATLEQFCVW 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGRVAGNNVLT G RGGVYIVGGV+PRFADFF SGFA+ F KGCMS Y +PVWLVT Sbjct: 241 LGRVAGNNVLTLGARGGVYIVGGVVPRFADFFAASGFARGFTSKGCMSRYLGDVPVWLVT 300 Query: 301 APYSGLTGAGVALEQAFA 318 A + GL GAGVALEQA A Sbjct: 301 AEFPGLEGAGVALEQALA 318 Lambda K H 0.320 0.139 0.429 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: 371 Number of extensions: 11 Number of successful extensions: 1 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: 318 Length of database: 319 Length adjustment: 27 Effective length of query: 291 Effective length of database: 292 Effective search space: 84972 Effective search space used: 84972 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: 48 (23.1 bits)
Align candidate GFF836 Psest_0850 (glucokinase, proteobacterial type)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))
# 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/TIGR00749.hmm # target sequence database: /tmp/gapView.28529.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00749 [M=315] Accession: TIGR00749 Description: glk: glucokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-82 262.3 0.1 3.7e-82 262.1 0.1 1.0 1 lcl|FitnessBrowser__psRCH2:GFF836 Psest_0850 glucokinase, proteoba Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF836 Psest_0850 glucokinase, proteobacterial type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.1 0.1 3.7e-82 3.7e-82 1 315 [] 5 310 .. 5 310 .. 0.96 Alignments for each domain: == domain 1 score: 262.1 bits; conditional E-value: 3.7e-82 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnld 76 lvgdiGGtnar+al ++e+v+++ + df e +v +yl + +c+a a+P+ g+ +tn++ lcl|FitnessBrowser__psRCH2:GFF836 5 LVGDIGGTNARFAL--WRDSRLESVRVLAAADFATPEMAVEYYLASLGLAPGSVEAACLACAGPVKGEQFTFTNNH 78 89************..677889***********************99999999779******************** PP TIGR00749 77 WalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgrykv 152 W l+ + l + +l lindfaa+a++++ ++e ++ + ++e++a+ ++G+GtGlGva l++ + g++++ lcl|FitnessBrowser__psRCH2:GFF836 79 WRLTRSDFCGALQMGELLLINDFAAMALGMTRVGEAGRRMICAGEAEPDAPALVIGPGTGLGVAGLLPLGGGSWRA 154 **************************************************************************** PP TIGR00749 153 lageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdiseaal 228 l+geGghvd+ + e+ l+++l +++g+v ae vlsG Gl l+y+ + l + +++ aal lcl|FitnessBrowser__psRCH2:GFF836 155 LPGEGGHVDLPVADAHEAALWQMLFAQLGHVRAEDVLSGGGLLLLYRTVCTVA------GLAPRLASPAEVTAAAL 224 ************************************************99876......45555569********* PP TIGR00749 229 egsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvv 304 +g++v a +le f++ lG++agn l+lgarGGvy++GG+vPrf +++ +s+f +f kG + +l+++Pv +v lcl|FitnessBrowser__psRCH2:GFF836 225 AGDHV-AVATLEQFCVWLGRVAGNNVLTLGARGGVYIVGGVVPRFADFFAASGFARGFTSKGCMSRYLGDVPVWLV 299 **987.5689****************************************************************** PP TIGR00749 305 lkkkvGllGag 315 + +Gl Gag lcl|FitnessBrowser__psRCH2:GFF836 300 TAEFPGLEGAG 310 *********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (319 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: 7.06 // [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