Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_029909212.1 P166_RS0104590 glucokinase
Query= curated2:B2J224 (341 letters) >NCBI__GCF_000711315.1:WP_029909212.1 Length = 327 Score = 190 bits (483), Expect = 4e-53 Identities = 117/333 (35%), Positives = 177/333 (53%), Gaps = 21/333 (6%) Query: 1 MTLLLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPIPE 60 M LLA D+G TK LV D++ HT+ Q+ Y SADF L ++Q F + + + Sbjct: 1 MGKLLAVDVGATKV---LVSAFDAETDHTLAQKRYLSADFSSLSKLIQTFQEEFSYSHFD 57 Query: 61 KACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDLH 120 AC +AGP+ LTNL W +D + L ++ I ++ ++NDFAA GI+ L ++D Sbjct: 58 VACLGLAGPVSARQVHLTNLPWIVDADVLAEDCHIDYVEIMNDFAAAALGINELSEEDTV 117 Query: 121 PLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYL 180 LQ G I+GAG+GLG + G + PSEGGH DFAP + + +L +L Sbjct: 118 CLQTGDYDAAGNKLIVGAGSGLGISPIKNCGGEFIPQPSEGGHMDFAPLDSTQLKLFDWL 177 Query: 181 LDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPG 240 K +S ER++SG GI +Y F ++ I + Sbjct: 178 HKKWT--HVSYERILSGEGIEFLYAFFNAENHGHSHHNLTPICSAEQ------------- 222 Query: 241 AAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNS 300 + A+ K + ++++TL F+E YGA GN++L G+YIAGGI PKI +Q Sbjct: 223 --VHELAM-KGEPIAQKTLNTFVEVYGAYIGNVSLLWQAKAGVYIAGGIGPKIRDWMQQP 279 Query: 301 GFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIG 333 F+ + T KGRM L+++IPVY+++N Q+GL+G Sbjct: 280 RFIRSMTAKGRMSGLVKDIPVYLVVNDQIGLLG 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: 259 Number of extensions: 10 Number of successful extensions: 4 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: 327 Length adjustment: 28 Effective length of query: 313 Effective length of database: 299 Effective search space: 93587 Effective search space used: 93587 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_029909212.1 P166_RS0104590 (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.16114.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-74 236.3 0.0 3.1e-74 236.0 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029909212.1 P166_RS0104590 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029909212.1 P166_RS0104590 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 236.0 0.0 3.1e-74 3.1e-74 1 313 [. 5 312 .. 5 314 .. 0.97 Alignments for each domain: == domain 1 score: 236.0 bits; conditional E-value: 3.1e-74 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdf 69 l+ d+G t+ ++ + + + + k y s df sl+++++ ++ee + d +c+ +a+P+ lcl|NCBI__GCF_000711315.1:WP_029909212.1 5 LAVDVGATKVLVSAFDAETDHTLAQKRYLSADFSSLSKLIQTFQEEFSYSHFD--VACLGLAGPVSARQ 71 688*********9999999999999*********************9999998..8************* PP TIGR00749 70 vrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlG 138 v+ltnl W + + l+++ + +e++ndfaa a++i l eed + l++ + + ++ + i+GaG GlG lcl|NCBI__GCF_000711315.1:WP_029909212.1 72 VHLTNLPWIVDADVLAEDCHIDYVEIMNDFAAAALGINELSEEDTVCLQTGDYDAAGNKLIVGAGSGLG 140 ********************************************************************* PP TIGR00749 139 vatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkge 207 ++ i++ g + ++eGgh dfaP + ++ l+++l+kk+ +vs er+lsG G+ +y +++ ++ lcl|NCBI__GCF_000711315.1:WP_029909212.1 141 ISP-IKNCGGEFIPQPSEGGHMDFAPLDSTQLKLFDWLHKKWTHVSYERILSGEGIEFLYAFFNAENHG 208 *97.678*********************************************************99988 PP TIGR00749 208 revsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiel 276 + l+ +++ e a++g+ ++a+++l++f+ ++Ga gn++l a+ Gvy+aGGi P++ ++ lcl|NCBI__GCF_000711315.1:WP_029909212.1 209 HSHHNLT-PICSAEQVHELAMKGE-PIAQKTLNTFVEVYGAYIGNVSLLWQAKAGVYIAGGIGPKIRDW 275 8888888.66777789*****996.89****************************************** PP TIGR00749 277 lkkssfraafedkGrlkellasiPvqvvlkkkvGllG 313 +++ f ++ kGr+ l+++iPv++v+++++GllG lcl|NCBI__GCF_000711315.1:WP_029909212.1 276 MQQPRFIRSMTAKGRMSGLVKDIPVYLVVNDQIGLLG 312 ***********************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (327 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: 10.84 // [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