Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate Pf1N1B4_600 Glucokinase (EC 2.7.1.2)
Query= reanno::WCS417:GFF4431 (318 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 Length = 319 Score = 563 bits (1450), Expect = e-165 Identities = 272/316 (86%), Positives = 293/316 (92%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 +KLALVGDIGGTNARFALW++Q+L S++V ATADH+SPE+AI +YL GL G IG+VC Sbjct: 1 LKLALVGDIGGTNARFALWKNQQLESVQVLATADHASPEEAIALYLSGLGLAPGSIGSVC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 LSVAGPVSGDEFKFTNNHWRLS+ FCKTLQVD+LLLVNDFSAMALGMTRL+P EFRVVC Sbjct: 61 LSVAGPVSGDEFKFTNNHWRLSRQGFCKTLQVDQLLLVNDFSAMALGMTRLQPGEFRVVC 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 EGTPEPLRPAVVIGPGTGLGVGTLLDLG GRFA LPGEGGHVDLPLSSPRETQLWQHI+ Sbjct: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGEGRFAPLPGEGGHVDLPLSSPRETQLWQHIFN 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 EIGHVSAETALSG GLPR+YRAICAVDGHTPVL+TPEAIT AGLAGDP+A+EVL+QF W Sbjct: 181 EIGHVSAETALSGSGLPRVYRAICAVDGHTPVLDTPEAITKAGLAGDPIALEVLEQFCCW 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGRVAGNNVLTTG RGGVYIVGGVIPRFADFFI SGFA+ FADKGCMSDYFKGIPVWLVT Sbjct: 241 LGRVAGNNVLTTGARGGVYIVGGVIPRFADFFIESGFARCFADKGCMSDYFKGIPVWLVT 300 Query: 301 APYSGLTGAGVALEQA 316 APYSGL GAGVALEQ+ Sbjct: 301 APYSGLVGAGVALEQS 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: 452 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 Pf1N1B4_600 (Glucokinase (EC 2.7.1.2))
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.2088787.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-80 257.3 0.0 1.2e-80 257.1 0.0 1.0 1 FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.1 0.0 1.2e-80 1.2e-80 1 315 [] 5 310 .. 5 310 .. 0.97 Alignments for each domain: == domain 1 score: 257.1 bits; conditional E-value: 1.2e-80 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaiatPiigd 68 lvgdiGGtnar+al +++e+v+++ + d+ s e+++ +yl+ + i c+++a+P+ gd FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 5 LVGDIGGTNARFAL--WKNQQLESVQVLATADHASPEEAIALYLSGLGLAPGS-IgSVCLSVAGPVSGD 70 89************..8899**************************9999998.5499*********** PP TIGR00749 69 fvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGl 137 ++tn++W ls + ++l + +l l+ndf+a+a++++ l+ ++ ++ +e+ + ++G+GtGl FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 71 EFKFTNNHWRLSRQGFCKTLQVDQLLLVNDFSAMALGMTRLQPGEFRVVCEGTPEPLRPAVVIGPGTGL 139 ********************************************************************* PP TIGR00749 138 GvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkg 206 Gv tl++ ++gr+ l+geGghvd+ s+ e++l++ + +++g+vsae lsGsGl +y+a+ +g FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 140 GVGTLLDLGEGRFAPLPGEGGHVDLPLSSPRETQLWQHIFNEIGHVSAETALSGSGLPRVYRAICAVDG 208 *******************************************************************96 PP TIGR00749 207 erevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfie 275 + v l +++ i++a l+g+ ++a + le f+ lG++agn l+ garGGvy++GG++Prf + FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 209 HTPV--L----DTPEAITKAGLAGD-PIALEVLEQFCCWLGRVAGNNVLTTGARGGVYIVGGVIPRFAD 270 6544..3....5899********96.89999************************************** PP TIGR00749 276 llkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 ++ +s+f f dkG + ++++ iPv +v Gl+Gag FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 271 FFIESGFARCFADKGCMSDYFKGIPVWLVTAPYSGLVGAG 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.49 // [ok]
This GapMind analysis is from Apr 09 2024. 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