Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate PP_1011 PP_1011 glucokinase
Query= reanno::WCS417:GFF4431 (318 letters) >FitnessBrowser__Putida:PP_1011 Length = 319 Score = 449 bits (1156), Expect = e-131 Identities = 218/316 (68%), Positives = 258/316 (81%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 MK LVGDIGGTNARFALWRD +LH + V AT D+++PE AI+ YL+ +G+ G + AVC Sbjct: 1 MKHLLVGDIGGTNARFALWRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 L+VAGPV GDEF+FTNNHWRLS+TAFCKTLQV+ LLL+NDF+AMALGMTRL+ EFR VC Sbjct: 61 LAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVC 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 G +P RPA+VIGPGTGLGVG+LL LG + ALPGEGGHVDLP+ + RE + Q I++ Sbjct: 121 PGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAAIHQQIHS 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 +IGHVSAE LSGGGL RLY+AICA+DG TP +TP IT A L G+P A+ V++QF + Sbjct: 181 QIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGEPRALAVVEQFCRF 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGRVAGNNVLT G RGGVYIVGGVIPRFA+ F+ SGFA SFADKGCMS YF G+PVWLVT Sbjct: 241 LGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVPVWLVT 300 Query: 301 APYSGLTGAGVALEQA 316 A +SGL GAGVAL+QA Sbjct: 301 AEFSGLEGAGVALQQA 316 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: 388 Number of extensions: 12 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 PP_1011 PP_1011 (glucokinase)
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.7890.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-82 261.8 0.0 5.3e-82 261.5 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1011 PP_1011 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1011 PP_1011 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.5 0.0 5.3e-82 5.3e-82 1 315 [] 5 310 .. 5 310 .. 0.97 Alignments for each domain: == domain 1 score: 261.5 bits; conditional E-value: 5.3e-82 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnl 75 lvgdiGGtnar+al +++ v+++ + d+ + e+++ yle + + + c+a+a+P+ gd r+tn+ lcl|FitnessBrowser__Putida:PP_1011 5 LVGDIGGTNARFAL--WRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVCLAVAGPVDGDEFRFTNN 77 89************..8899****************************999998899****************** PP TIGR00749 76 dWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgry 150 +W ls ++l +++l lindf+a+a++++ l+e ++ + ++++s + ++G+GtGlGv l++ +++ + lcl|FitnessBrowser__Putida:PP_1011 78 HWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVCPGQADPSRPALVIGPGTGLGVGSLLRLGEQLW 152 *************************************************************************** PP TIGR00749 151 kvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdise 225 k+l+geGghvd+ + e+ + + +++++g+vsae vlsG Glv +y+a+ +g+ + ++++ i++ lcl|FitnessBrowser__Putida:PP_1011 153 KALPGEGGHVDLPVGNAREAAIHQQIHSQIGHVSAEAVLSGGGLVRLYQAICALDGDT-----P-RHKTPAHITD 221 *****************************************************99654.....3.456899**** PP TIGR00749 226 aalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiP 300 aal g+ + a +e f+ lG++agn l+lgarGGvy++GG++Prf el+ +s+f a+f dkG + +++ +P lcl|FitnessBrowser__Putida:PP_1011 222 AALGGE-PRALAVVEQFCRFLGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVP 295 ***875.788899************************************************************** PP TIGR00749 301 vqvvlkkkvGllGag 315 v +v + Gl Gag lcl|FitnessBrowser__Putida:PP_1011 296 VWLVTAEFSGLEGAG 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.79 // [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