Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate AO356_05215 AO356_05215 glucokinase
Query= reanno::WCS417:GFF4431 (318 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05215 Length = 318 Score = 555 bits (1430), Expect = e-163 Identities = 268/318 (84%), Positives = 294/318 (92%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 +KLALVGDIGGTNARFALW+D L +I+V ATAD++ PEDAI+VYL GL+ G IG+VC Sbjct: 1 LKLALVGDIGGTNARFALWKDHTLENIQVLATADYACPEDAIQVYLGGLGLKPGAIGSVC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 LSVAGPVSGDEF+FTNNHWRLS AFCKTLQV++LLLVNDFSAMALGMT L+PDE+RVVC Sbjct: 61 LSVAGPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVVC 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 EGTPEP+RPAVVIGPGTGLGVGTLLDLG GRFAALPGEGGHVDLP+SSPRETQLWQHIY Sbjct: 121 EGTPEPMRPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIYN 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 EIGHVSAETALSG GLPR+YRAICAVDGH PVL+TPE+ITAAGLAGDP+A+EVL+QF W Sbjct: 181 EIGHVSAETALSGSGLPRVYRAICAVDGHVPVLDTPESITAAGLAGDPIALEVLEQFCRW 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGRVAGNNVLT GGRGGVYIVGGV+PRFADFF+ SGFA+ FADKGCMSDYFKGIPVWLVT Sbjct: 241 LGRVAGNNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVT 300 Query: 301 APYSGLTGAGVALEQAFA 318 APYSGL GAGVALEQ+ A Sbjct: 301 APYSGLMGAGVALEQSAA 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: 465 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: 318 Length adjustment: 27 Effective length of query: 291 Effective length of database: 291 Effective search space: 84681 Effective search space used: 84681 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 AO356_05215 AO356_05215 (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.17642.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-82 261.7 0.0 5.4e-82 261.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 AO356_05215 glucokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 AO356_05215 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.5 0.0 5.4e-82 5.4e-82 1 315 [] 5 310 .. 5 310 .. 0.96 Alignments for each domain: == domain 1 score: 261.5 bits; conditional E-value: 5.4e-82 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaia 62 lvgdiGGtnar+al +e+++++ + d+ e++++vyl + + i c+++a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 5 LVGDIGGTNARFAL--WKDHTLENIQVLATADYACPEDAIQVYLGGLGLKPGA-IgSVCLSVA 64 89************..78899***********************999888887.5599***** PP TIGR00749 63 tPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakvees 125 +P+ gd r+tn++W ls ++l ++kl l+ndf+a+a++++ l+ ++ ++ +e+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 65 GPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVVCEGTPEPM 127 *************************************************************** PP TIGR00749 126 aaiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaerv 188 + ++G+GtGlGv tl++ ++gr+ +l+geGghvd+ s+ e++l++ + +++g+vsae lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 128 RPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIYNEIGHVSAETA 190 *************************************************************** PP TIGR00749 189 lsGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalag 251 lsGsGl +y+a+ +g +v l +++ i+ a l+g+ ++a + le f+ lG++ag lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 191 LSGSGLPRVYRAICAVDG--HVPVLD----TPESITAAGLAGD-PIALEVLEQFCRWLGRVAG 246 ***************994..344455....99*********96.89999************** PP TIGR00749 252 nlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGa 314 n l+lg rGGvy++GG+vPrf +++ +s+f f dkG + ++++ iPv +v Gl+Ga lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 247 NNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVTAPYSGLMGA 309 **************************************************************9 PP TIGR00749 315 g 315 g lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 310 G 310 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (318 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.15 // [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