Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_011766044.1 AZO_RS11675 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000061505.1:WP_011766044.1 Length = 317 Score = 197 bits (502), Expect = 2e-55 Identities = 122/338 (36%), Positives = 179/338 (52%), Gaps = 28/338 (8%) Query: 4 LLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPIPEKAC 63 +LA DIGG+++ L L E + + T+ + ++ S DF + ++ FL T AC Sbjct: 3 ILAADIGGSQSRLLLAEL-EGEAWRTLRRHTFPSPDFASVEALLDGFLAGGETVAA--AC 59 Query: 64 FAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDLHPLQ 123 A+AGP+ LTNL W +D L G+ + ++NDFAA +G+ L + LQ Sbjct: 60 LAVAGPVASQRVALTNLPWIVDAAALATRFGLRQVRIVNDFAAQAHGLPALDADGICTLQ 119 Query: 124 VGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYLLDK 183 G P + ++GAGTGLG L + + PSEGGHADFAPRN E L++ LL + Sbjct: 120 AGAPVADGLRALMGAGTGLGVALLAGPDAHPRALPSEGGHADFAPRNAEEMALVQDLLPR 179 Query: 184 HDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPGAAI 243 H RIS+E ++ G G+ +Y+ + AG + + AI Sbjct: 180 HG--RISLETLLCGRGLERLYR----------------------RAAGLADDAPASARAI 215 Query: 244 GTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNSGFL 303 G AAL + + + LF GA AGNLAL L GG+Y++GGI PK+LPL+++ G Sbjct: 216 GEAAL-AGEPAARDAVALFGRLLGAAAGNLALTSLALGGVYLSGGITPKLLPLLRDGGLR 274 Query: 304 LNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAARL 341 F K MR L+E IP++++ + +GL GAA AARL Sbjct: 275 EAFCDKPPMRALMERIPLHVVTDELLGLKGAAQLAARL 312 Lambda K H 0.320 0.140 0.408 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: 264 Number of extensions: 13 Number of successful extensions: 2 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: 341 Length of database: 317 Length adjustment: 28 Effective length of query: 313 Effective length of database: 289 Effective search space: 90457 Effective search space used: 90457 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: 49 (23.5 bits)
Align candidate WP_011766044.1 AZO_RS11675 (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.13680.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-73 231.5 0.0 9.9e-73 231.1 0.0 1.1 1 lcl|NCBI__GCF_000061505.1:WP_011766044.1 AZO_RS11675 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011766044.1 AZO_RS11675 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.1 0.0 9.9e-73 9.9e-73 1 315 [] 4 306 .. 4 306 .. 0.94 Alignments for each domain: == domain 1 score: 231.1 bits; conditional E-value: 9.9e-73 TIGR00749 1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 l++diGG ++rl l e +++ +t+ s+df s+ea++ +l +++ +c+a+a+P+ lcl|NCBI__GCF_000061505.1:WP_011766044.1 4 LAADIGGSQSRLLLAELEGEAWRTLrrHTFPSPDFASVEALLDGFLAGGETVA-A---ACLAVAGPVAS 68 79*************9998888888779******************9876554.4...7********** PP TIGR00749 68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtG 136 + v+ltnl W + + l+ ++l+++ ++ndfaa+a +++al+ + + l++ ++ ++ a++GaGtG lcl|NCBI__GCF_000061505.1:WP_011766044.1 69 QRVALTNLPWIVDAAALATRFGLRQVRIVNDFAAQAHGLPALDADGICTLQAGAPVADGLRALMGAGTG 137 ********************************************************************* PP TIGR00749 137 lGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrk 205 lGva l d + ++l++eGgh+dfaPr+ +e+ l++ l + gr+s e +l G Gl +y+ lcl|NCBI__GCF_000061505.1:WP_011766044.1 138 LGVALLAG-PDAHPRALPSEGGHADFAPRNAEEMALVQDLLPRHGRISLETLLCGRGLERLYRRA---A 202 ***98887.9****************************************************754...3 PP TIGR00749 206 gerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfi 274 g+ + + + i eaal+g+ + ar a+ lf +lGa agnlal+ +a GGvy++GGi P+++ lcl|NCBI__GCF_000061505.1:WP_011766044.1 203 GLAD-----DAPASARAIGEAALAGE-PAARDAVALFGRLLGAAAGNLALTSLALGGVYLSGGITPKLL 265 3332.....44567899*******97.789*************************************** PP TIGR00749 275 ellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 +ll+ +++r+af dk +++l++ iP++vv ++ Gl Ga+ lcl|NCBI__GCF_000061505.1:WP_011766044.1 266 PLLRDGGLREAFCDKPPMRALMERIPLHVVTDELLGLKGAA 306 ***************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (317 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: 00:00:00.00 # Mc/sec: 10.35 // [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