Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate PfGW456L13_1890 Glucokinase (EC 2.7.1.2)
Query= reanno::WCS417:GFF4431 (318 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 Length = 319 Score = 566 bits (1459), Expect = e-166 Identities = 274/316 (86%), Positives = 296/316 (93%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 +KLALVGDIGGTNARFALW++Q+L S++V ATAD SPE+AI +YL GL G IG+VC Sbjct: 1 LKLALVGDIGGTNARFALWKNQQLESVQVLATADFPSPEEAISLYLNGLGLAPGSIGSVC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 LSVAGPVSGDEFKFTNNHWRLS+ FC+TLQVD+LLLVNDFSAMALGMTRL+P EFRVVC Sbjct: 61 LSVAGPVSGDEFKFTNNHWRLSRKGFCQTLQVDQLLLVNDFSAMALGMTRLQPGEFRVVC 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHI+ Sbjct: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIFN 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 EIGHVSAETALSGGGLPR+YRAICAVDGHTPVL+TPEAITAAGLAGDP+A+EVL+QF W Sbjct: 181 EIGHVSAETALSGGGLPRVYRAICAVDGHTPVLDTPEAITAAGLAGDPIAVEVLEQFCCW 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFF+ SGFA+ FADKGCMSDYFKGIPVWLVT Sbjct: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVT 300 Query: 301 APYSGLTGAGVALEQA 316 APYSGL GAGVALEQ+ Sbjct: 301 APYSGLMGAGVALEQS 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: 458 Number of extensions: 8 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 PfGW456L13_1890 (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.3425.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-81 258.7 0.0 4.6e-81 258.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 Glucokinase (EC 2.7.1.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 Glucokinase (EC 2.7.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.5 0.0 4.6e-81 4.6e-81 1 315 [] 5 310 .. 5 310 .. 0.97 Alignments for each domain: == domain 1 score: 258.5 bits; conditional E-value: 4.6e-81 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi 55 lvgdiGGtnar+al +++e+v+++ + dfps e+++ +yl+ + i lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 5 LVGDIGGTNARFAL--WKNQQLESVQVLATADFPSPEEAISLYLNGLGLAPGS-I 56 89************..8899**************************9999998.5 PP TIGR00749 56 .kgcfaiatPiigdfvrltnldWalsieelkqelalaklelindfaavayailal 109 c+++a+P+ gd ++tn++W ls + q+l + +l l+ndf+a+a++++ l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 57 gSVCLSVAGPVSGDEFKFTNNHWRLSRKGFCQTLQVDQLLLVNDFSAMALGMTRL 111 499**************************************************** PP TIGR00749 110 keedliqlggakveesaaiailGaGtGlGvatliqqsdgrykvlageGghvdfaP 164 + ++ ++ +e+ + ++G+GtGlGv tl++ + gr+ +l+geGghvd+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 112 QPGEFRVVCEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPL 166 ******************************************************* PP TIGR00749 165 rseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219 s+ e++l++ + +++g+vsae lsG Gl +y+a+ +g+ v l + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 167 SSPRETQLWQHIFNEIGHVSAETALSGGGLPRVYRAICAVDGHTPV--L----DT 215 ****************************************966544..3....58 PP TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfi 274 ++ i+ a l+g+ ++a + le f+ lG++agn l+ g rGGvy++GG++Prf lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 216 PEAITAAGLAGD-PIAVEVLEQFCCWLGRVAGNNVLTTGGRGGVYIVGGVIPRFA 269 99********96.78999************************************* PP TIGR00749 275 ellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 +++ +s+f f dkG + ++++ iPv +v Gl+Gag lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1890 270 DFFLESGFARCFADKGCMSDYFKGIPVWLVTAPYSGLMGAG 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: 10.02 // [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