Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_012852101.1 TCUR_RS08615 glucokinase
Query= reanno::WCS417:GFF4431 (318 letters) >NCBI__GCF_000024385.1:WP_012852101.1 Length = 326 Score = 216 bits (549), Expect = 8e-61 Identities = 132/314 (42%), Positives = 167/314 (53%), Gaps = 11/314 (3%) Query: 5 LVGDIGGTNARFALWRDQELHSIRVHATA--DHSSPEDAIKVYLKEEGLEIGDI--GAVC 60 LV DIGGTNARF L + RV A DH+ +A YL GD+ GA C Sbjct: 13 LVADIGGTNARFGLIQAPGAPPSRVQVLALRDHAGLAEATATYLARHA---GDVRPGAAC 69 Query: 61 LSVAGPVSGD-EFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVV 119 ++VAGPV+ D F+ TN HW S L +D + L+NDF A+AL + L+P + RV+ Sbjct: 70 VAVAGPVTDDGRFQLTNAHWSGSAEEVRADLGLDHVELINDFEALALALPTLQPGDLRVL 129 Query: 120 CEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIY 179 E P PA V+GPGTGLGV L+ G R A+P EGGHVDLP ++PRE +L + Sbjct: 130 GERAPGGQTPAAVLGPGTGLGVAALVRAGE-RLVAIPSEGGHVDLPATTPRELELAAMLR 188 Query: 180 TEIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSI 239 E G AE LSG G+ RLY I + H ++ A DP+ E L+ F Sbjct: 189 EEHGTAEAERLLSGEGMTRLYELIARM--HAVPVQPLSAAQICARRSDPLCQETLETFCA 246 Query: 240 WLGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLV 299 LG AGN LT G RGGVY+ GG++PR D S F + F K M Y + IP L+ Sbjct: 247 LLGSFAGNVALTFGARGGVYLGGGILPRIWDVLRRSDFRRRFESKPPMERYLRAIPTALI 306 Query: 300 TAPYSGLTGAGVAL 313 AP L GA L Sbjct: 307 VAPTPALAGAAARL 320 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: 286 Number of extensions: 14 Number of successful extensions: 5 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: 326 Length adjustment: 28 Effective length of query: 290 Effective length of database: 298 Effective search space: 86420 Effective search space used: 86420 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 WP_012852101.1 TCUR_RS08615 (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.24298.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-83 267.1 0.0 1.4e-83 266.7 0.0 1.1 1 lcl|NCBI__GCF_000024385.1:WP_012852101.1 TCUR_RS08615 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012852101.1 TCUR_RS08615 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 266.7 0.0 1.4e-83 1.4e-83 1 315 [] 13 317 .. 13 317 .. 0.95 Alignments for each domain: == domain 1 score: 266.7 bits; conditional E-value: 1.4e-83 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigd. 68 lv+diGGtnar++l++ + v+++ d+ l ++ yl +++ ++ p +c+a+a+P+++d lcl|NCBI__GCF_000024385.1:WP_012852101.1 13 LVADIGGTNARFGLIQAPGAPPSRVQVLALRDHAGLAEATATYLARHAGDVR-PGAACVAVAGPVTDDg 80 89************988888899**************************997.699**********994 PP TIGR00749 69 fvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGl 137 +ltn +W+ s ee++ +l+l ++elindf a a+a+++l+ dl +lg + +++ a+lG+GtGl lcl|NCBI__GCF_000024385.1:WP_012852101.1 81 RFQLTNAHWSGSAEEVRADLGLDHVELINDFEALALALPTLQPGDLRVLGERAPGGQTPAAVLGPGTGL 149 68******************************************************************* PP TIGR00749 138 GvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkg 206 Gva l++ + +r++++++eGghvd+ + + e+ l +lr++ g aer+lsG G+ +ye + + + lcl|NCBI__GCF_000024385.1:WP_012852101.1 150 GVAALVR-AGERLVAIPSEGGHVDLPATTPRELELAAMLREEHGTAEAERLLSGEGMTRLYELIARMH- 216 *******.7889***************************************************99887. PP TIGR00749 207 erevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfie 275 ++ ++ sd+l++++le+f+++lG++agn+al++garGGvy+ GGi+Pr+ + lcl|NCBI__GCF_000024385.1:WP_012852101.1 217 A--------VPVQPLSAAQICARRSDPLCQETLETFCALLGSFAGNVALTFGARGGVYLGGGILPRIWD 277 2........2345555667777889******************************************** PP TIGR00749 276 llkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 l++s fr +fe k ++ +l iP +++ ++ l Ga+ lcl|NCBI__GCF_000024385.1:WP_012852101.1 278 VLRRSDFRRRFESKPPMERYLRAIPTALIVAPTPALAGAA 317 **************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (326 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: 6.97 // [ok]
This GapMind analysis is from Sep 24 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